annotate feelnc2asko.xml @ 0:e323c49b8bcc draft

planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241

<tool id="feelnc2asko" name="Convert FeelNC GTF" version="0.1">
    <description>to GFF3 for AskOmics</description>
    <requirements>
        <requirement type="package" version="1.6.924">perl-bioperl</requirement>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[
        perl '$__tool_directory__/feelnc2asko.pl' --ann '${anngff}' --lnc '${lncgtf}' --new '${newgtf}' > '${outgff}'
    ]]></command>

    <inputs>
        <param format="gff" name="anngff" type="data" label="Initial annotation file" />
        <param format="gtf" name="lncgtf" type="data" label="FeelNC lncRNA annotation" />
        <param format="gtf" name="newgtf" type="data" label="FeelNC new mRNA annotation" />
    </inputs>

    <outputs>
        <data format="gff" name="outgff" label="${tool.name} on ${on_string} : FeelNC GFF" />
    </outputs>

    <tests>
        <test>
            <param name="anngff" ftype="gff" value="initial.gff3" />
            <param name="lncgtf" ftype="gtf" value="feelnc_lncRNA.gtf" />
            <param name="newgtf" ftype="gtf" value="feelnc_mRNA.gtf" />
            <output name="outgff" ftype="gff" file="completeAnnot.gff3" compare="sim_size" />
        </test>
    </tests>

    <help>
        Generates a GFF compliant to AskOmics from the FeelNC output files merged with the initial annotation file.
    </help>

    <citations>
    </citations>
</tool>