Mercurial > repos > frogs > frogs_2_0_0
diff r_composition.xml @ 0:76c750c5f0d1 draft default tip
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
| author | frogs |
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| date | Thu, 25 Oct 2018 05:01:13 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/r_composition.xml Thu Oct 25 05:01:13 2018 -0400 @@ -0,0 +1,151 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2017 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool id="FROGSSTAT_Phyloseq_Composition_Visualisation" name="FROGSSTAT Phyloseq Composition Visualisation" version="1.0.0"> + <description>with bar plot and composition plot</description> + <requirements> + <requirement type="package" version="2.0.1">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command>r_composition.py + --rdata $data + --varExp $varExp + --taxaRank1 $taxaRank1 + --taxaSet1 $taxaSet1 + --taxaRank2 $taxaRank2 + --numberOfTaxa $numberOfTaxa + --html $html + </command> + <inputs> + <!-- Files --> + <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <!-- Parameters --> + <param name="varExp" type="text" label="Grouping variable" help="Experimental variable used to group samples (Treatment, Host type, etc)." optional="false" value="" size="20"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <param name="taxaRank1" type="text" label="Taxonomic level to filter your data" help="ex: Kingdom, Phylum, Class, Order, Family, Genus, Species" value="Kingdom" size="20"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <param name="taxaSet1" type="text" label="Taxa (at the above taxonomic level) to keep in the dataset" help="ex: Bacteria (when filtering at the Kingdom level), Firmicutes (when filtering at the Phylum level). Multiple taxa (separated by a space) can be specified, i.e. Firmicutes Proteobacteria" value="Bacteria" size="20"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <param name="taxaRank2" type="text" label="Taxonomic level used for aggregation" help="ex: Family (when filtering at the Phylum level). The aggregation level must be below the filtering level." value="Phylum" size="20"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <param name="numberOfTaxa" type="text" label="Number of most abundant taxa to keep" help="ex: 9, i.e. Tool keeps the 9 most abundant taxa and the remaining taxa are aggregated in a group 'Other'" value="9" size="20"> + <validator type="empty_field" message="This parameter is required." /> + </param> + </inputs> + <outputs> + <data format="html" name="html" label="${tool.name}: composition.html" from_work_dir="composition.html"/> + </outputs> + <tests> + <test> + <param name="data" value="references/11-phylo_import.Rdata" /> + <param name="varExp" value="EnvType" /> + <param name="taxaRank1" value="Kingdom" /> + <param name="taxaSet1" value="Bacteria" /> + <param name="taxaRank2" value="Phylum" /> + <param name="numberOfTaxa" value="9" /> + <!--output name="html" file="references/12-phylo_composition.html" compare="sim_size" delta="0" /--> + <output name="html"> + <assert_contents> + <has_text_matching expression="html\sxmlns=.*" /> + <has_text_matching expression="application/json.*Sample: BHT0.LOT01" /> + </assert_contents> + </output> + </test> + </tests> + <help> +.. image:: static/images/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and custom R function, this tool constructs two plots to visualise the sample composition: one at the OTU level and another one at the specified aggregation level (*e.g.* Phylum) after keeping only a subset of taxa (*e.g.* Bacteria at the level Kingdom). It helps answer the question: "What is the composition at the Phylum level within Bacteria?". By default, the plot exhibits only the abundance of the 9 most abundant taxa (as specified). In general, the representation of more than 10 taxa is hard to read on plots. + + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**data file** (format rdata): +One phyloseq object containing the OTU abundance table, their taxonomies and optionnaly a phylogenetic tree, and the sample experiment metadata. +this file is the result of FROGS Phyloseq Import Data tool. + +.. class:: h3 + +Output + +**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): data composition plots. + +Bar plot of OTUs is colored with aggregated taxonomic level *i.e* "Phylum" : + + .. image:: static/images/phyloseq_bar_plot.png + :height: 646 + :width: 800 + +Composition plot: plot the most abundant sub taxonomic level among a selection of OTUs. + +- Selection of OTUs: + + - Taxonomic level name to subset: Kingdom + - Taxon name: Bacteria + +- Aggregation of OTUs : + + - Taxonomic level used to agglomerate: Phylum + +- Number of the most abundant taxa to keep: 5 + + .. image:: static/images/phyloseq_composition_plot.png + :height: 644 + :width: 800 + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS + +Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf + +Depending on the help provided you can cite us in acknowledgements, references or both. + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + <citation type="doi">10.1128/AEM.01043-13</citation> + <citation type="doi">10.14806/ej.17.1.200</citation> + <citation type="doi">10.1093/bioinformatics/btr507</citation> + </citations> + +</tool>