<?xml version="1.0"?>
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# Copyright (C) 2017 INRA
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# 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
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-->
<tool id="FROGS_Tree" name="FROGS Tree" version="@TOOL_VERSION@+galaxy2">
    <description>Reconstruction of phylogenetic tree </description>

      <macros>
          <import>macros.xml</import>
      </macros>

      <expand macro="requirements" >
          <requirement type="package" version="7.407">mafft</requirement>
          <requirement type="package" version="2.1.9">fasttree</requirement>
          <requirement type="package" version="4.0">r-essentials</requirement>
          <requirement type="package" version="2.7.0">r-phangorn</requirement>
      </expand>

    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <command>
        tree.py
            --input-sequences '$input_otu'
            --biom-file '$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}: report.html" from_work_dir="summary.html"/>
    </outputs>
    <tests>
        <test>
            <param name="input_otu" value="references/09-normalisation.fasta"/>
            <param name="biomfile" value="references/09-normalisation.biom"/>
            <output name="out_tree" value="references/15-tree-mafft.nwk" compare="sim_size" delta="30"/>
            <output name="html" value="references/15-tree-mafft.html" compare="diff" lines_diff="2"/>
            <output name="html" value="references/15-tree-mafft.html" compare="sim_size" delta="30"/>
            <output name="html">
                 <assert_contents>
                    <has_text_matching expression="FROGS\sTree" />
                    <has_text_matching expression="abundance_removed.*:\s0" />
                    <has_text_matching expression="abundance_kept.*:\s300" />
                    <has_text_matching expression="otu_removed.*:\s0" />
                    <has_text_matching expression="otu_kept.*:\s52" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
@HELP_LOGO@

.. 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_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 `nwk or nhx &lt;https://en.wikipedia.org/wiki/Newick_format&gt;`_).

 .. image:: static/images/FROGS_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

@HELP_CONTACT@



    </help>

    <citations>
        <expand macro="citations" />
    </citations>
    
</tool>