<?xml version="1.0"?>
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# Copyright (C) 2017 INRA
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<tool id="FROGS_Tree" name="FROGS Tree" version="1.0.0">
	<description>Reconstruction of phylogenetic tree </description>
 	<requirements>
                <requirement type="package" version="2.0.1">frogs</requirement>
        </requirements>
        <stdio>
                <exit_code range="1:" />
                <exit_code range=":-1" />
        </stdio>
	<command>tree.py 
                                            --input-otu $input_otu
                                              #if $template.fileTemplate
                                            --template-pynast ${template.template_pynast}
                                              #end if
                                            --biomfile $biomfile
                                            --nb-cpus $nb_cpus
                                            --out-tree $out_tree
                                            --html $html
	</command>
    <inputs>
		<!-- Files -->
	<param format="fasta" name="input_otu" type="data" label="OTUs sequence file" help="OTUs sequence file (format: fasta). Warning: FROGS Tree does not work on more than 10000 sequences!" optional="false">
            <validator type="empty_field" message="This parameter is required." />
        </param>
	<conditional name="template">
		<param name="fileTemplate" type="boolean" label="Do you have the template alignment file ?" help="If yes, precise the template multi-alignment file." optional="false" />
		<when value="false"></when>           
		<when value="true">
			<param format="fasta" name="template_pynast" type="data" label="Template alignment file" help="Template multi-alignment file (format: fasta)." optional="false" />
		</when>
	</conditional>
        <param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance table of OTUs (format: biom)." optional="false">
        	<validator type="empty_field" message="This parameter is required." />
        </param>
        <!-- Parameter -->
        <param name="nb_cpus" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1" />	
    	</inputs>
	<outputs>
		<data format="nhx" name="out_tree" label="${tool.name}: tree.nwk" from_work_dir="tree.nwk"/>
        	<data format="html" name="html" label="${tool.name}: summary.html" from_work_dir="summary.html"/>
	</outputs>
	<tests>
		<test>
			<param name="input_otu" value="references/04-filters.fasta"/>
			<conditional name="template">
				<param name="fileTemplate" value="false"/>
			</conditional>
			<param name="biomfile" value="references/04-affiliation.biom"/>
			<output name="out_tree" value="references/10b-tree.nwk"/>
		</test>
	</tests>
	<help>
.. image:: static/images/FROGS_logo.png 
   :height: 144
   :width: 110

.. class:: infomark page-header h2

What it does

Creation of a multiple alignment of OTUs with `PyNAST &lt;http://biocore.github.io/pynast/&gt;`_ (if you have an alignment template file) or with `Mafft &lt;http://mafft.cbrc.jp/alignment/software&gt;`_ (if you have not an aligned template file).
And creation of a phylogenetic tree with `FastTree &lt;http://www.microbesonline.org/fasttree/&gt;`_.

.. class:: infomark page-header h2

Inputs/Outputs

.. class:: h3

Input

**OTUs fasta file**:

The OTUs sequence file (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
Careful: FROGS Tree works only with less than 10 000 sequences!
 
 .. image:: static/images/frogs_tree_otufile.png

**(optional) Template alignment file**:

A pre-aligned database of sequences (the “template” sequence) (format `multiple alignement &lt;https://en.wikipedia.org/wiki/Multiple_sequence_alignment&gt;`_).

 .. image:: static/images/frogs_tree_templatefile.png 
     
**OTUs biom file**:

The OTUs biom file (format `biom1 &lt;http://biom-format.org/documentation/format_versions/biom-1.0.html&gt;`_).
This file can be obtained in particular with the FROGS pipeline.

.. class:: h3

Outputs

**Newick file** (tree.nwk):

The phylogenetic tree in Newick format (format `nxh &lt;https://en.wikipedia.org/wiki/Newick_format&gt;`_).

 .. image:: static/images/nwk_treefile.png

**Html file** (summary.html):
   
The summary file describing which OTUs are contained or not in the phylogenetic tree (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).

.. 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">10.7287/peerj.preprints.386v1</citation>
	</citations>
</tool>