tree.xml

<?xml version="1.0"?>
<!--
# Copyright (C) 2017 INRA
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-->
<tool id="FROGS_Tree" name="FROGS Tree" version="3.1">
	<description>Reconstruction of phylogenetic tree </description>
 	<requirements>
                <requirement type="package" version="3.1.0">frogs</requirement>
        </requirements>
        <stdio>
                <exit_code range="1:" />
                <exit_code range=":-1" />
        </stdio>
	<command>tree.py 
                                            --input-otu $input_otu
                                            --biomfile $biomfile
                                            --nb-cpus \${GALAXY_SLOTS:-1}
                                            --out-tree $out_tree
                                            --html $html
	</command>
    <inputs>
	<!-- Files -->
	<param format="fasta" name="input_otu" type="data" label="OTUs sequence file" help="OTUs sequence file (format: fasta). Warning: FROGS Tree does not work on more than 10000 sequences!" optional="false">
        	<validator type="empty_field" message="This parameter is required." />
        </param>
        <param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance table of OTUs (format: biom)." optional="false">
        	<validator type="empty_field" message="This parameter is required." />
        </param>
    </inputs>
	<outputs>
		<data format="nhx" name="out_tree" label="${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"/>
			<param name="biomfile" value="references/06-affiliation.biom"/>
			<!--output name="out_tree" value="references/13-tree-mafft.nwk"/-->
			<!--output name="html" value="references/13-tree-mafft.html"/-->
			<output name="html">
 		        	<assert_contents>
                    		<has_text_matching expression="FROGS\sTree" />
                    		<has_text_matching expression="abundance_removed.*:\s0" />
                    		<has_text_matching expression="abundance_kept.*:\s45574" />
                    		<has_text_matching expression="otu_removed.*:\s0" />
                    		<has_text_matching expression="otu_kept.*:\s86" />
                		</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

Creation of a multiple alignment of OTUs with `Mafft &lt;http://mafft.cbrc.jp/alignment/software&gt;`_.
And creation of a rooted phylogenetic tree with `FastTree &lt;http://www.microbesonline.org/fasttree/&gt;`_ and `Phangorn R package &lt;https://cran.r-project.org/web/packages/phangorn/index.html&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_images/frogs_tree_otufile.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/frogs_images/nwk_treefile.png

**Html file** (summary.html):
   
The summary file describing which OTUs are contained or not in the phylogenetic tree.

.. class:: infomark page-header h2
   
**Contact**

Contacts: frogs@inra.fr

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>