annotate GAFA.xml @ 0:af9f72ddf7f9 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ commit 822c798d43a72724eeab174043fdaafcfdac845f-dirty

<tool id="gafa" name="Gene Align and Family Aggregator" version="0.1.0">
    <description>generates an SQLite database that can be visualised with Aequatus</description>
    <command>
<![CDATA[
python '$__tool_directory__/GAFA.py'
#for $dataset in $treeFile:
    -t '$dataset'
#end for
#for $dataset in $alignmentFile:
    -c '$dataset'
#end for
-g '$genesFile'
-o '$outputFile'
]]>
    </command>
    <inputs>
        <param name="treeFile" type="data" format="nhx" 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="tabular" multiple="true" label="CDS alignments" help="CDS alignments in tabular format generated by 'T-Coffee to CIGAR' tool" />
        <param name="genesFile" type="data" format="json" label="Gene features" help="Gene features in JSON format generated by 'GFF3 to JSON' or 'Get Ensembl features by ID' tool" />
    </inputs>
    <outputs>
        <data name="outputFile" format="gafa.sqlite" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="treeFile" ftype="nhx" value="tree.nhx" />
            <param name="alignmentFile" ftype="tabular" value="cigar.tabular" />
            <param name="genesFile" ftype="json" value="gene.json" />
            <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 "CDS alignments" dataset by removing everything from the first underscore to the end of the string.

.. _Aequatus: http://aequatus.earlham.ac.uk
]]>
    </help>
    <citations>
    </citations>
</tool>