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planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
author frogs
date Thu, 25 Oct 2018 05:01:13 -0400
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76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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1 # Copyright (C) 2014 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
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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5 # the Free Software Foundation, either version 3 of the License, or
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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6 # (at your option) any later version.
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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7 #
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8 # This program is distributed in the hope that it will be useful,
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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9 # but WITHOUT ANY WARRANTY; without even the implied warranty of
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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10 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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11 # GNU General Public License for more details.
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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12 #
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13 # You should have received a copy of the GNU General Public License
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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14 # along with this program. If not, see <http://www.gnu.org/licenses/>.
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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15 #
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16 #
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17 #This is a sample file that enables tools FROGS_affiliations_OTU to use taxonomy database for
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18 #taxonomy affiliation. You will need to create or download Blast+ index and train your database
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19 #for RDP classifier these data files.
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20 #download link : http://genoweb.toulouse.inra.fr/frogs_databanks/assignation
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21 #Finally you will need to create frogs_db.loc file similar to this one in your galaxy
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22 #tool-data directory.The frogs_db.loc file has this format (longer white space characters are
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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23 #TAB characters):
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24 #
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25 #<unique_database_name> <file_path>
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26 #
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27 #First column will be the visible name in galaxy.
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28 #So, for example, if you had 16S silva 128 indexed stored in
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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29 #/galaxy_databanks/16S/silva_128/
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30 #then the frogs_db.loc entry would look like this:
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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31 #
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32 #silva 128 16S /galaxy_databanks/16S/silva_128/silva_128_16S.fasta
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33 #
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34 #and your /galaxy_databanks/16S/silva_128/ directory
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35 #would contain index files:
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36 #
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37 #-rw-r--r-- 1 mbernard FROGS 8097966 5 déc. 16:56 bergeyTrainingTree.xml
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38 #-rw-r--r-- 1 mbernard FROGS 1572981589 5 déc. 16:56 genus_wordConditionalProbList.txt
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39 #-rw-r--r-- 1 mbernard FROGS 1654 5 déc. 16:56 LICENCE.txt
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40 #-rw-r--r-- 1 mbernard FROGS 1072228 5 déc. 16:56 logWordPrior.txt
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41 #-rw-r--r-- 1 mbernard FROGS 940834335 5 déc. 16:56 silva_128_16S.fasta
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42 #-rw-r--r-- 1 mbernard FROGS 152606489 5 déc. 16:56 silva_128_16S.fasta.nhr
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43 #-rw-r--r-- 1 mbernard FROGS 6918588 5 déc. 16:56 silva_128_16S.fasta.nin
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44 #-rw-r--r-- 1 mbernard FROGS 205320030 5 déc. 16:56 silva_128_16S.fasta.nsq
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45 #-rw-r--r-- 1 mbernard FROGS 281 5 déc. 16:56 silva_128_16S.fasta.properties
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46 #-rw-r--r-- 1 mbernard FROGS 3420464 5 déc. 16:56 silva_128_16S.tax
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47 #-rw-r--r-- 1 mbernard FROGS 964048 5 déc. 16:57 wordConditionalProbIndexArr.txt
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48 #
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49 #
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50 #<name> <name> <file_path>
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51 #
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52 #db.fasta db.fasta db.fasta ${__HERE__}/test-data/db.fasta
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53 #db.fasta db.fasta db.fasta /root/mydisk/FROGS-wrappers/test-data/db.fasta
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54 db.fasta db.fasta /root/mydisk/FROGS-wrappers/test-data/db.fasta