<tool id="gafa" name="Gene Align and Family Aggregator" version="0.4.0">
    <description>generates an SQLite database that can be visualised with Aequatus</description>
    <requirements>
        <requirement type="package" version="3.13">python</requirement>
    </requirements>
    <command detect_errors="exit_code">
<![CDATA[
python3 '$__tool_directory__/GAFA.py'
#for $dataset in $treeFile:
    -t '$dataset'
#end for
#for $dataset in $alignmentFile:
    -a '$dataset'
#end for
-g '$genesFile'
-o '$outputFile'
]]>
    </command>
    <inputs>
        <param name="treeFile" type="data" format="nhx,newick" multiple="true" label="Gene tree" help="Gene tree in Newick format, e.g. generated from 'TreeBeST best' or 'Get gene tree by Ensembl ID' tool" />
        <param name="alignmentFile" type="data" format="fasta" multiple="true" label="Protein alignments" help="Protein alignments in fasta_aln format generated by T-Coffee" />
        <param name="genesFile" type="data" format="sqlite" label="Gene features" help="Gene features in SQLite format generated by 'GSTF preparation' tool" />
    </inputs>
    <outputs>
        <data name="outputFile" format="gafa.sqlite" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="treeFile" ftype="nhx" value="tree1.nhx,tree2.nhx,tree3.nhx,tree4.nhx" />
            <param name="alignmentFile" ftype="fasta" value="align1.fasta,align2.fasta,align3.fasta,align4.fasta" />
            <param name="genesFile" ftype="sqlite" value="gene.sqlite" />
            <output name="outputFile" file="test.gafa.sqlite" compare="sim_size" />
        </test>
    </tests>
    <help>
<![CDATA[
Simple tool to generate an SQLite database that can be visualised with `Aequatus`_.

Aequatus is an open-source homology browser developed with novel rendering approaches to visualise homologous, orthologous and paralogous gene structures.

N.B.: The tool will modify the sequence identifiers found in the "Protein alignments" dataset by removing everything from the first underscore to the end of the string.

.. _Aequatus: https://github.com/TGAC/Aequatus
]]>
    </help>
    <citations>
        <citation type="doi">https://doi.org/10.1093/gigascience/giy005</citation>
    </citations>
</tool>