view tree.xml @ 4:445b04a65ed8 draft

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3

<tool id="FROGS_Tree" name="FROGS Tree" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05">
    <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="4.1.2">r-base</requirement>
        <requirement type="package" version="4.1">r-essentials</requirement>
        <requirement type="package" version="2.7.0">r-phangorn</requirement>
    </expand>
    <command detect_errors="exit_code">
        tree.py
            --input-sequences '$input_otu'
            --biom-file '$biomfile'
            @CPUS@
            --out-tree '$out_tree'
            --html '$html'
    </command>
    <inputs>
        <!-- Files -->
        <param format="fasta" name="input_otu" type="data" label="Sequence file" help="Sequence file (format: FASTA). Warning: FROGS Tree does not work on more than 10000 sequences!"/>
        <param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance file (format: BIOM)"/>
    </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.*:\s74781" />
                    <has_text_matching expression="otu_removed.*:\s0" />
                    <has_text_matching expression="otu_kept.*:\s55" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
@HELP_LOGO@

.. class:: infomark page-header h2

What it does

This tool creates a multiple alignment of OTUs with `Mafft &lt;http://mafft.cbrc.jp/alignment/software&gt;`_.
And creates 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

**Fasta file**:

The OTU 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:: FROGS_tree_otufile.png

**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:: FROGS_nwk_treefile.png

**Report file** (report.html):

The report file describing which OTUs are contained or not in the phylogenetic tree.

.. class:: infomark page-header h2

@HELP_CONTACT@



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