Mercurial > repos > frogs > frogs
annotate phyloseq_import_data.xml @ 8:0966b9635d76 draft default tip
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 43fa7e46c98b5d5d7915f86524d4c0c4f501d782
author | frogs |
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date | Wed, 14 Jun 2023 14:56:49 +0000 |
parents | b2967b704d6b |
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445b04a65ed8
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3
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1 <tool id="FROGSSTAT_Phyloseq_Import_Data" name="FROGSSTAT Phyloseq Import Data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> |
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b2967b704d6b
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit af85e2b40a89d997ccbf0310ca51cc71489d334e
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2 <description>from 3 files: biomfile, samplefile, treefile </description> |
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8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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3 <macros> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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4 <import>macros.xml</import> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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5 </macros> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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6 <expand macro="requirements_phyloseq" /> |
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445b04a65ed8
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3
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7 <command detect_errors="exit_code"> |
445b04a65ed8
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3
frogs
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8 phyloseq_import_data.py |
445b04a65ed8
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3
frogs
parents:
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9 --biomfile '$biomfile' |
445b04a65ed8
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3
frogs
parents:
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10 --samplefile '$samplefile' |
445b04a65ed8
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3
frogs
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11 #if $treefile |
445b04a65ed8
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3
frogs
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12 --treefile '$treefile' |
445b04a65ed8
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3
frogs
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13 #end if |
445b04a65ed8
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3
frogs
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14 --ranks $ranks |
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b2967b704d6b
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit af85e2b40a89d997ccbf0310ca51cc71489d334e
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15 #if $normalisation == "true" |
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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3
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16 --normalisation |
445b04a65ed8
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3
frogs
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17 #end if |
445b04a65ed8
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3
frogs
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18 --html '$html' |
445b04a65ed8
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3
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19 --rdata '$data' |
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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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20 </command> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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21 <inputs> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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22 <!-- Files --> |
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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit af85e2b40a89d997ccbf0310ca51cc71489d334e
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23 <param format="biom1" argument="--biomfile" type="data" label="Abundance biom file with taxonomical metadata (format: BIOM)" help="The file contains the ASV information "/> |
b2967b704d6b
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit af85e2b40a89d997ccbf0310ca51cc71489d334e
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24 <param format="tabular,tsv" argument="--samplefile" type="data" label="Metadata associated to samples (format: TSV)" help="The file contains the metadata that characterise each sample."/> |
b2967b704d6b
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit af85e2b40a89d997ccbf0310ca51cc71489d334e
frogs
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25 <param format="nhx" argument="--treefile" type="data" optional="true" label="Taxonomic tree file (format: Newick)" help="The file contains the taxonomic tree information from FROGS Tree tool (optional)"/> |
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445b04a65ed8
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3
frogs
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26 <!-- Parameters --> |
445b04a65ed8
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3
frogs
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27 <param argument="--ranks" type="text" value="Kingdom Phylum Class Order Family Genus Species" |
445b04a65ed8
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3
frogs
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28 label="Names of taxonomic levels" help="The ordered taxonomic levels stored in BIOM. Each level is separated by one space"> |
445b04a65ed8
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3
frogs
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29 <expand macro="sanitizer_validator"/> |
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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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30 </param> |
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b2967b704d6b
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit af85e2b40a89d997ccbf0310ca51cc71489d334e
frogs
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31 <param argument="--normalisation" type="select" label="Do you want to normalise your data ?" help="To normalise data before statistical analysis (default : No)" display="radio"> |
b2967b704d6b
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit af85e2b40a89d997ccbf0310ca51cc71489d334e
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32 <option value="false">No, keep abundance as it is.</option> |
b2967b704d6b
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit af85e2b40a89d997ccbf0310ca51cc71489d334e
frogs
parents:
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33 <option value="true">Yes, subsample abundances to the smallest sample size.</option> |
b2967b704d6b
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit af85e2b40a89d997ccbf0310ca51cc71489d334e
frogs
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34 </param> |
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834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
frogs
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35 </inputs> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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36 <outputs> |
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b2967b704d6b
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit af85e2b40a89d997ccbf0310ca51cc71489d334e
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37 <data format="rdata" name="data" label="${tool.name}: asv_data.Rdata" from_work_dir="asv_data.Rdata"/> |
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445b04a65ed8
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3
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38 <data format="html" name="html" label="${tool.name}: report.nb.html" from_work_dir="report.nb.html"/> |
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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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39 </outputs> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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40 <tests> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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41 <test> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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42 <param name="biomfile" value="input/chaillou.biom"/> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
frogs
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43 <param name="samplefile" value="input/sample_metadata.tsv"/> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
frogs
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44 <param name="treefile" value="input/tree.nwk"/> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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45 <output name="data" value="references/16-phylo_import.Rdata" compare="sim_size" delta="10"/> |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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46 <!-- <output name="html" value="references/16-phylo_import.nb.html" compare="diff" lines_diff="0"/> --> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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47 <output name="html"> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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48 <assert_contents> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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49 <!-- check phyloseq object summary--> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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50 <has_text text='otu_table() OTU Table: [ 508 taxa and 64 samples ]'/> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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51 <has_text text='sample_data() Sample Data: [ 64 samples by 4 sample variables ]' /> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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52 <has_text text='tax_table() Taxonomy Table: [ 508 taxa by 7 taxonomic ranks ]' /> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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53 <has_text text='phy_tree() Phylogenetic Tree: [ 508 tips and 507 internal nodes ]' /> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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54 <!-- check phyloseq object rank names--> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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55 <has_text text='Rank names : Kingdom, Phylum, Class, Order, Family, Genus, Species'/> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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56 <!-- check phyloseq object Sample variables--> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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57 <has_text text='Sample variables: EnvType, Description, FoodType, SampleID'/> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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58 <!-- check phyloseq object Variables details--> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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59 <has_text text='EnvType : BoeufHache, VeauHache, DesLardons, MerguezVolaille, SaumonFume, FiletSaumon, FiletCabillaud, Crevette'/> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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60 <has_text text='Description : LOT1, LOT3, LOT4, LOT5, LOT6, LOT7, LOT8, LOT10, LOT2, LOT9'/> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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61 <has_text text='FoodType : Meat, Seafood'/> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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62 <has_text text='SampleID : BHT0.LOT01, BHT0.LOT03, BHT0.LOT04, BHT0.LOT05, BHT0.LOT06, BHT0.LOT07, BHT0.LOT08, BHT0.LOT10, VHT0.LOT01, VHT0.LOT02, VHT0.LOT03, VHT0.LOT04, VHT0.LOT06, VHT0.LOT07, VHT0.LOT08, VHT0.LOT10, DLT0.LOT01, DLT0.LOT03, DLT0.LOT04, DLT0.LOT05, DLT0.LOT06, DLT0.LOT07, DLT0.LOT08, DLT0.LOT10, MVT0.LOT01, MVT0.LOT03, MVT0.LOT05, MVT0.LOT06, MVT0.LOT07, MVT0.LOT08, MVT0.LOT09, MVT0.LOT10, SFT0.LOT01, SFT0.LOT02, SFT0.LOT03, SFT0.LOT04, SFT0.LOT05, SFT0.LOT06, SFT0.LOT07, SFT0.LOT08, FST0.LOT01, FST0.LOT02, FST0.LOT03, FST0.LOT05, FST0.LOT06, FST0.LOT07, FST0.LOT08, FST0.LOT10, FCT0.LOT01, FCT0.LOT02, FCT0.LOT03, FCT0.LOT05, FCT0.LOT06, FCT0.LOT07, FCT0.LOT08, FCT0.LOT10, CDT0.LOT02, CDT0.LOT04, CDT0.LOT05, CDT0.LOT06, CDT0.LOT07, CDT0.LOT08, CDT0.LOT09, CDT0.LOT10'/> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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63 </assert_contents> |
8edcbafb3b4e
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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64 </output> |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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65 </test> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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66 </tests> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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67 <help> |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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68 |
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69 @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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70 |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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71 .. class:: infomark page-header h2 |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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72 |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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73 What it does |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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74 |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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75 Launch Rmarkdown script to import data from 3 files: biomfile, samplefile, treefile into a `phyloseq <https://joey711.github.io/phyloseq/>`_ object. |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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76 |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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77 .. class:: infomark page-header h2 |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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78 |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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79 Inputs/Outputs |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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80 |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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81 .. class:: h3 |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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82 |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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83 Input |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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84 |
6
b2967b704d6b
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit af85e2b40a89d997ccbf0310ca51cc71489d334e
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85 **ASV abundance file (in biom format)**: |
0
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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86 |
6
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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit af85e2b40a89d997ccbf0310ca51cc71489d334e
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87 The ASV biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). |
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88 The example of biom file: |
0
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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89 |
4
445b04a65ed8
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3
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90 .. image:: FROGS_Phyloseq_biomfile.png |
0
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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91 :height: 30 |
3
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"
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92 :width: 733 |
0
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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93 |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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94 **Newick file** (tree.nwk): |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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95 |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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96 Newick file (format `nxh <https://en.wikipedia.org/wiki/Newick_format>`_) is the result of FROGS Tree: |
834843ebe569
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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97 |
4
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98 .. image:: FROGS_nwk_treefile.png |
0
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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99 |
6
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100 **Metadata file**: |
0
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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101 The file contains the conditions of experiment with sample ID in the first column: |
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102 |
4
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103 .. image:: FROGS_Phyloseq_samplefile.png |
0
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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104 :height: 115 |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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105 :width: 369 |
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106 |
0
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107 .. class:: h3 |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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108 |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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109 Output |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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110 |
6
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111 **Html report file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): The summary of phyloseq object. |
3
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112 |
4
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113 .. image:: FROGS_Phyloseq_import_data_html.png |
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114 |
6
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115 **Data file** (format Rdata): The information of data in one phyloseq object. |
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116 |
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117 |
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118 .. class:: infomark page-header h2 |
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119 |
3
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120 @HELP_CONTACT@ |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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121 |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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122 </help> |
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123 <expand macro="citations" /> |
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"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"
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124 </tool> |