Mercurial > repos > frogs > frogs
annotate deseq2_preprocess.xml @ 3:8edcbafb3b4e draft
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
author | frogs |
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date | Tue, 24 Aug 2021 08:21:23 +0000 |
parents | 094a2469204d |
children | 445b04a65ed8 |
rev | line source |
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0
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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1 <?xml version="1.0"?> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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2 <!-- |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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3 # Copyright (C) 2017 INRA |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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4 # |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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5 # This program is free software: you can redistribute it and/or modify |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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6 # it under the terms of the GNU General Public License as published by |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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7 # the Free Software Foundation, either version 3 of the License, or |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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8 # (at your option) any later version. |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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9 # |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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10 # This program is distributed in the hope that it will be useful, |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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11 # but WITHOUT ANY WARRANTY; without even the implied warranty of |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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13 # GNU General Public License for more details. |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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14 # |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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15 # You should have received a copy of the GNU General Public License |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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16 # along with this program. If not, see <http://www.gnu.org/licenses/>. |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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17 --> |
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8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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18 <tool id="FROGSSTAT_DESeq2_Preprocess" name="FROGSSTAT DESeq2 Preprocess" version="@TOOL_VERSION@+galaxy2"> |
0
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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19 <description>import a Phyloseq object and prepare it for DESeq2 differential abundance analysis </description> |
3
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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20 |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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21 <macros> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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22 <import>macros.xml</import> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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23 </macros> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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24 |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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25 <expand macro="requirements_phyloseq"> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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26 <requirement type="package" version="1.30.1">bioconductor-deseq2</requirement> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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27 <requirement type="package" version="1.6.6">r-optparse</requirement> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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28 </expand> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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29 |
0
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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30 <stdio> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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31 <exit_code range="1:" /> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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32 <exit_code range=":-1" /> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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33 </stdio> |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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34 <command>deseq2_preprocess.py --data '$data' |
0
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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35 #if $multiple.seconde |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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36 --var '$var1${multiple.mod}${multiple.var2}' |
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834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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37 #else |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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38 --var '$var1' |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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39 #end if |
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8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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40 --out-Rdata '$dds' |
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834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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41 </command> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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42 <inputs> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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43 <!-- Files --> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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44 <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGSSTAT Phyloseq Import Data with normalise option set to NO (DESeq2 is more powerful on unnormalised counts)." optional="false"> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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45 <validator type="empty_field" message="This parameter is required." /> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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46 </param> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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47 <!-- Parameters --> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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48 <param name="var1" type="text" label="Experimental variable" help="The factor suspected to have an effect on OTUs' abundances. Ex: Treatment, etc." optional="false" value="" size="20"> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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49 <validator type="empty_field" message="This parameter is required." /> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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50 </param> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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51 <conditional name="multiple"> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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52 <param name="seconde" type="boolean" label="Do you want to correct for a confounding factor?" help="If yes, specifiy counfouding factor." optional="false" /> |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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53 <when value="false"></when> |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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54 <when value="true"> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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55 <param name="var2" type="text" label="Variable 2" help="Confounding factor. Ex: Gender, etc." optional="false" value="" size="20"/> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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56 <param name="mod" type="select" multiple="false" help="Choose an additive model (+) if the effects of Treatment and Gender are independent. Choose a model with interaction (*) if the effect of Treatment is expected to depend on Gender." label="Type of model"> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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57 <option value="+" selected="true">Linear (+)</option> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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58 <option value="*">Interaction (*)</option> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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59 </param> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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60 </when> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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61 </conditional> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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62 </inputs> |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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63 <outputs> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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64 <data format="rdata" name="dds" label="${tool.name}: dds.Rdata" from_work_dir="DESeq2_preprocess.Rdata"/> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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65 </outputs> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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66 <tests> |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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67 <test> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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68 <param name="data" value="references/16-phylo_import.Rdata" /> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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69 <param name="var1" value="EnvType"/> |
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70 <output name="dds" file="references/23-deseq2_preprocess.Rdata" compare="sim_size" delta="50"/> |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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71 </test> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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72 </tests> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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73 <help> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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74 |
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75 @HELP_LOGO@ |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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76 |
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77 .. class:: infomark page-header h2 |
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78 |
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79 What it does |
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80 |
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81 Launch Rscript to compute differential abundance analysis using `DESeq2 <https://bioconductor.org/packages/release/bioc/html/DESeq2.html>`_ on a `Phyloseq <https://joey711.github.io/phyloseq/>`_ object. |
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82 |
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83 .. class:: infomark page-header h2 |
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84 |
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85 Inputs/Outputs |
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86 |
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87 .. class:: h3 |
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88 |
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89 Input |
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90 |
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91 **phyloseq object** (format rdata): |
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92 A phyloseq object stored in a rdata file. |
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93 This file is the result of FROGSSTAT Phyloseq Import Data. |
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94 |
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95 .. class:: warningmark |
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96 |
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97 We need unnormalised data to analyse the abundance differencies. |
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98 |
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99 .. class:: h3 |
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100 |
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101 Ouput |
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102 |
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103 **dds object** (format rdata): |
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104 A DESeq2 dataset (dds) stored in rdata file. |
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105 This result will be one of the input of the FROGSSTAT DESeq Visualisation tool. |
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106 |
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107 .. class:: infomark page-header h2 |
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108 |
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109 How it works |
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110 |
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111 The DESeq function performs a default analysis through the steps: |
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112 |
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113 1. estimation of size factors: ‘estimateSizeFactors’ |
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114 |
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115 2. estimation of dispersion: ‘estimateDispersions’ |
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116 |
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117 3. Negative Binomial GLM fitting and Wald statistics: |
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118 ‘nbinomWaldTest’ |
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119 |
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120 You must precise at least on variable on which the differential abundances will be compared. |
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121 |
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122 You may precise a confounding factor, by adding an other variable and precise the relation between the two variables: |
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123 |
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124 - + for independant variables |
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125 - * for interacting variables |
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126 |
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127 @HELP_CONTACT@ |
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128 |
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129 </help> |
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130 |
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131 <citations> |
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132 <expand macro="citations" /> |
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133 </citations> |
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134 |
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135 </tool> |