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r_composition.xml
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r_composition.xml
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<?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="3.1">
<description>with bar plot and composition plot</description>
<requirements>
<requirement type="package" version="3.1.0">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/14-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/15-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_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/frogs_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/frogs_images/phyloseq_composition_plot.png
:height: 644
:width: 800
.. class:: infomark page-header h2
**Contact**
Contacts: [email protected]
Repository: https://github.com/geraldinepascal/FROGS
website: http://frogs.toulouse.inra.fr/
Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*
</help>
<citations>
<citation type="doi">10.1093/bioinformatics/btx791</citation>
</citations>
</tool>