<tool id="pangolin" name="Pangolin" version="@VERSION@+galaxy0">
    <description> CoV-2019 Phylogenetic Assignment of Named Global Outbreak LINeages</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

pangolin '$input1' -t "\${GALAXY_SLOTS:-1}" --max-ambig '$additional.max_ambig' --min-length '$additional.min_length' &&

sed 's/,/\t/g' lineage_report.csv > lineage_report.tsv
    ]]></command>
    <inputs>
        <param name="input1" type="data" format="fasta"
            label="Input multi-sequence fasta file"
            />
        <section name="additional" title="Additional Parameters" expanded="false">
            <param name="max_ambig" type="float" value="0.5" min="0" max="1.0"
                label="Maximum proportion of Ns allowed to attempt assignment"
                argument="--max-ambig"
                />
            <param name="min_length" type="integer" value="10000" min="0"
                label="Minimum query length to attempt assignment"
                argument="--min-length"
                />
        </section>
    </inputs>
    <outputs>
        <data format="tabular" from_work_dir="lineage_report.tsv" name="lineage_report" label="${input1.name}_lineage_report" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="test_seqs.fasta" />
            <output name="lineage_report" value="lineage_report.tsv" />
        </test>
    </tests>
    <help><![CDATA[
    
Pangolin
--------

Pangolin assigns SARS-CoV-2 genome sequences in fasta format to global lineages from `Rambaut et al. <https://doi.org/10.1101/2020.04.17.046086>`_.
To do this, Pangolin employs the use of external programs including: `iqtree <http://www.iqtree.org/#download>`_, `mafft <https://mafft.cbrc.jp/alignment/software/>`_,
and `snakemake <https://snakemake.readthedocs.io/en/stable/index.html>`_.

More information can be obtained from the authors github site: https://github.com/hCoV-2019/pangolin

--------------

**Input** - Multi sequence fasta file


**Output** - lineage report:

+---------+---------+------+-------------+------------------+-----------+-----------+
| Taxon   | Lineage | aLRT | UFbootstrap | lineages_version | status    | note      |
+=========+=========+======+=============+==================+===========+===========+
| Sample1 | A.1     | 100  | 60          | 2020-04-27       | passed_qc |           |
+---------+---------+------+-------------+------------------+-----------+-----------+
| Sample2 | B.1     | 80   | 80          | 2020-04-27       | passed_qc |           |
+---------+---------+------+-------------+------------------+-----------+-----------+
| Sample3 | B.1.4   | 60   | 100         | 2020-04-27       | fail      | seq_len:0 |
+---------+---------+------+-------------+------------------+-----------+-----------+


Resources for interpreting aLRT and UFbootstrap values:

- `IQ_TREE: Assessing branch supports with single branch tests <http://www.iqtree.org/doc/Tutorial#assessing-branch-supports-with-single-branch-tests>`_

- `IQ_TREE: Command Reference <http://www.iqtree.org/doc/Command-Reference>`_

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