Mercurial > repos > oinizan > frogs
annotate test-data/databases/frogs_picrust2_functions.loc @ 30:fce825ec2c84 draft default tip
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 01b92e7e17eb8bc125451bf41684f512cf16d3c5-dirty
| author | oinizan |
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| date | Fri, 02 May 2025 07:44:22 +0000 |
| parents | 646bee69560f |
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| rev | line source |
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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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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
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2 # |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
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3 # This program is free software: you can redistribute it and/or modify |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
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4 # it under the terms of the GNU General Public License as published by |
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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 |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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6 # (at your option) any later version. |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
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7 # |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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8 # This program is distributed in the hope that it will be useful, |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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9 # but WITHOUT ANY WARRANTY; without even the implied warranty of |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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10 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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11 # GNU General Public License for more details. |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
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12 # |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
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13 # You should have received a copy of the GNU General Public License |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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14 # along with this program. If not, see <http://www.gnu.org/licenses/>. |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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15 # |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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16 # |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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17 #This is a sample file that enables tools FROGS_frogsfunc_copynumbers to predict |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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18 #the copy number of gene families present in the predicted genome for OTU, |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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19 # given a tree and a set of known trait values (FROGS_frogsfunc_placeseqs). |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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20 # |
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646bee69560f
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit b6afc353bed8654c3a9ca56d194ecc7827d9ca18
oinizan
parents:
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21 #PICRUSt2 files are present in the arborescence of PICRUSt2. |
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646bee69560f
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit b6afc353bed8654c3a9ca56d194ecc7827d9ca18
oinizan
parents:
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22 # |
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646bee69560f
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit b6afc353bed8654c3a9ca56d194ecc7827d9ca18
oinizan
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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> <version> |
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646bee69560f
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit b6afc353bed8654c3a9ca56d194ecc7827d9ca18
oinizan
parents:
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24 |
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646bee69560f
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit b6afc353bed8654c3a9ca56d194ecc7827d9ca18
oinizan
parents:
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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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646bee69560f
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit b6afc353bed8654c3a9ca56d194ecc7827d9ca18
oinizan
parents:
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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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646bee69560f
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit b6afc353bed8654c3a9ca56d194ecc7827d9ca18
oinizan
parents:
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27 # |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff
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28 # |
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646bee69560f
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit b6afc353bed8654c3a9ca56d194ecc7827d9ca18
oinizan
parents:
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29 # Bellow you will find out how to implement this loc file. |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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30 # |
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646bee69560f
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit b6afc353bed8654c3a9ca56d194ecc7827d9ca18
oinizan
parents:
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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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646bee69560f
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit b6afc353bed8654c3a9ca56d194ecc7827d9ca18
oinizan
parents:
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32 # Just adapt path by replacing <Galaxy_dir> with the real path and eventually the picrust version. |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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33 # |
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646bee69560f
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit b6afc353bed8654c3a9ca56d194ecc7827d9ca18
oinizan
parents:
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diff
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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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646bee69560f
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit b6afc353bed8654c3a9ca56d194ecc7827d9ca18
oinizan
parents:
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35 # |
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646bee69560f
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit b6afc353bed8654c3a9ca56d194ecc7827d9ca18
oinizan
parents:
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36 # |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff
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37 # |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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38 # EXAMPLE FOR TEST : |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
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39 16S EC EC EC 2.5.1 |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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40 16S KO KO KO 2.5.1 |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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41 16S PFAM PFAM PFAM 2.5.1 |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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42 16S COG COG COG 2.5.1 |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
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43 16S TIGRFAM TIGRFAM TIGRFAM 2.5.1 |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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44 16S PHENO PHENO PHENO 2.5.1 |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
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45 ITS EC ${__HERE__}/frogs_picrust2_db/prokaryotic/16S_test.txt.gz ${__HERE__}/frogs_picrust2_db/prokaryotic/ec_test.txt.gz 2.5.1 |