Mercurial > repos > oinizan > frogs
annotate test-data/databases/frogs_picrust2_pathways.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
parents:
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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
parents:
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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
parents:
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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:
diff
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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
parents:
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12 # |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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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:
diff
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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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changeset
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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_pathways to map pathways to reactions. |
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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 default mapfile maps MetaCyc reactions to prokaryotic MetaCyc pathways. |
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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 # |
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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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20 #PICRUSt2 files are present in the arborescence of PICRUSt2. Please consult |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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21 #PICRUSt2 documentation to find out where they are located in your environment. |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff
changeset
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22 # |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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23 #If you are not comfortable with picrust2 command lines, just create .loc files |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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24 #with EXAMPLE FOR TEST files remembering to replace <PATH_TO> with the real path. |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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25 # |
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646bee69560f
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit b6afc353bed8654c3a9ca56d194ecc7827d9ca18
oinizan
parents:
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26 #<db_id> <db_name> <marker_gene> <path_to_mapfiles> <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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changeset
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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 #First column will be the visible name in galaxy. |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff
changeset
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29 # |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff
changeset
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30 # |
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dfaf556d2a20
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff
changeset
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31 # EXAMPLE FOR TEST : |
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646bee69560f
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit b6afc353bed8654c3a9ca56d194ecc7827d9ca18
oinizan
parents:
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32 pro_metacyc_pathway Metacyc 16S ${__HERE__}/frogs_picrust2_db/pathway_mapfiles/metacyc_path2rxn_struc_filt_pro.txt 2.5.1 |