<?xml version="1.0"?>
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<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 &lt;https://joey711.github.io/phyloseq/&gt;`_ 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 &lt;https://en.wikipedia.org/wiki/HTML&gt;`_): 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>