<tool id="ensembl_longest_cds_per_gene" name="Select longest CDS per gene" version="0.0.2">
    <description>from Ensembl CDS FASTA</description>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/ensembl_longest_cds_per_gene.py' -f '$input' -o '$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="fasta" label="CDS FASTA from Ensembl" />
    </inputs>
    <outputs>
        <data name="output" format="fasta" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="fasta" value="Mus_musculus.GRCm38.cds.first100.fa" />
            <output name="output" file="Mus_musculus.GRCm38.cds.longest.fa" />
        </test>
    </tests>
    <help><![CDATA[
This tool filters a CDS FASTA file from Ensembl retaining only the longest CDS sequence for each gene.

The headers of the input CDS FASTA file are expected to be of the following format::

    >ENSMUST00000177965.1 cds chromosome:GRCm38:12:113456720:113456736:-1 gene:ENSMUSG00000094057.1 gene_biotype:IG_D_gene transcript_biotype:IG_D_gene gene_symbol:Ighd2-7 description:immunoglobulin heavy diversity 2-7 [Source:MGI Symbol;Acc:MGI:4439866]

Among the CDS sequences having the same gene identifier (ENSMUSG00000094057 in the example above), the tool will select the one with the longest sequence.
    ]]></help>
</tool>