Mercurial > repos > frogs > frogs_3_1_0
annotate r_import_data.xml @ 0:59bc96331073 draft default tip
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
| author | frogs |
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| date | Thu, 28 Feb 2019 10:14:49 -0500 |
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| rev | line source |
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0
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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1 <?xml version="1.0"?> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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2 <!-- |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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3 # Copyright (C) 2017 INRA |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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4 # |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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5 # This program is free software: you can redistribute it and/or modify |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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6 # it under the terms of the GNU General Public License as published by |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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7 # the Free Software Foundation, either version 3 of the License, or |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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8 # (at your option) any later version. |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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9 # |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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10 # This program is distributed in the hope that it will be useful, |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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11 # but WITHOUT ANY WARRANTY; without even the implied warranty of |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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13 # GNU General Public License for more details. |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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14 # |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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15 # You should have received a copy of the GNU General Public License |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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16 # along with this program. If not, see <http://www.gnu.org/licenses/>. |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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17 --> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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18 <tool name="FROGSSTAT Phyloseq Import Data" id="FROGSSTAT_Phyloseq_Import_Data" version="3.1"> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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19 <description>from 3 files: biomfile, samplefile, treefile </description> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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20 <requirements> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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21 <requirement type="package" version="3.1.0">frogs</requirement> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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22 </requirements> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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23 <stdio> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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24 <exit_code range="1:" /> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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25 <exit_code range=":-1" /> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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26 </stdio> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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27 <command>r_import_data.py --biomfile $biomfile |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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28 |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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29 --samplefile $samplefile |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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30 #if $treefile |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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31 --treefile $treefile |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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32 #end if |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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33 --ranks "$ranks" |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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34 #if $normalization |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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35 --normalization |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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36 #end if |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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37 --html $html |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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38 --rdata $data |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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39 </command> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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40 <inputs> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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41 <!-- Files --> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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42 <param format="biom1" name="biomfile" type="data" label="Standard biom file" help="The file contains the OTU informations (format: biom1)." optional="false"> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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43 <validator type="empty_field" message="This parameter is required." /> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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44 </param> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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45 |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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46 <param format="tabular" name="samplefile" type="data" label="Sample tsv file" help="The file contains the samples informations (format: tabular)." optional="false"> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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47 <validator type="empty_field" message="This parameter is required." /> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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48 </param> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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49 |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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50 <param format="nhx" name="treefile" type="data" label="Tree file" help="The file contains the tree informations (format: Newick - nhx or nwk)." optional="true" /> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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51 |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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52 <!-- Parameters --> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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53 <param name="ranks" type="text" label="Names of taxonomics levels" help="The ordered taxonomic levels stored in BIOM. Each level is separated by one space." value="Kingdom Phylum Class Order Family Genus Species" size="80" optional="false"/> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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54 <param name="normalization" type="boolean" label="Do you want to normalise your data ?" help="To normalise data before analysis." optional="false" /> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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55 </inputs> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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56 <outputs> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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57 <data format="rdata" name="data" label="${tool.name}: data.Rdata" from_work_dir="data.Rdata"/> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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58 <data format="html" name="html" label="${tool.name}: summary.html" from_work_dir="summary.html"/> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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59 </outputs> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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60 <tests> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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61 <test> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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62 <param name="biomfile" value="input/chaillou.biom"/> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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63 <param name="samplefile" value="input/sample_metadata.tsv"/> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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64 <param name="treefile" value="input/tree.nwk"/> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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65 <output name="data" value="references/14-phylo_import.Rdata" compare="sim_size" delta="10"/> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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66 </test> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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67 </tests> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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68 <help> |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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69 |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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70 .. image:: static/images/frogs_images/FROGS_logo.png |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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71 :height: 144 |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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72 :width: 110 |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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73 |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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74 .. class:: infomark page-header h2 |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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75 |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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76 What it does |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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77 |
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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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78 Launch Rmarkdown script to import data from 3 files: biomfile, samplefile, treefile into a `phyloseq <https://joey711.github.io/phyloseq/>`_ object. |
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79 |
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80 .. class:: infomark page-header h2 |
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81 |
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82 Inputs/Outputs |
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83 |
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84 .. class:: h3 |
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85 |
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86 Input |
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87 |
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88 **OTU biom file**: |
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89 |
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90 The OTU biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). |
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91 This file is the result of FROGS BIOM to std BIOM. |
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92 The example of biom file: |
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93 |
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94 .. image:: static/images/frogs_images/biomfile.png |
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95 :height: 30 |
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96 :width: 733 |
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97 |
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98 **Newick file** (tree.nwk): |
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99 |
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100 Newick file (format `nxh <https://en.wikipedia.org/wiki/Newick_format>`_) is the result of FROGS Tree: |
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101 |
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102 .. image:: static/images/frogs_images/nwk_treefile.png |
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103 |
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104 **Sample file**: |
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105 The file contains the conditions of experiment with sample ID in the first column: |
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106 |
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107 .. image:: static/images/frogs_images/phyloseq_samplefile.png |
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108 :height: 115 |
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109 :width: 369 |
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110 |
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111 .. class:: h3 |
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112 |
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113 Output |
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114 |
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115 **Html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): The summary of phyloseq object. |
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116 |
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117 .. image:: static/images/frogs_images/phyloseq_import_data_html.png |
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118 |
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119 **Data file** (format rdata): The informations of data in one phyloseq object. |
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120 |
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121 |
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122 .. class:: infomark page-header h2 |
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123 |
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124 **Contact** |
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125 |
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126 Contacts: frogs@inra.fr |
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127 |
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128 Repository: https://github.com/geraldinepascal/FROGS |
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129 website: http://frogs.toulouse.inra.fr/ |
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130 |
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131 Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* |
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132 |
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133 </help> |
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134 <citations> |
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135 <citation type="doi">10.1093/bioinformatics/btx791</citation> |
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136 </citations> |
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137 |
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138 </tool> |