<tool id="longORF" name="Obtain longest ORFs" version="0.3.0">
    <description> in six-frame translations</description>
    <command><![CDATA[
        python $__tool_directory__/getLongestORF.py $input $output_longestORF $output_ORFs
    ]]>
    </command>
    <inputs>
        <param name="input" format="fasta" type="data" label="sequences"/>
    </inputs>
    <outputs>
        <data name="output_longestORF" format="fasta"/>
        <data name="output_ORFs" format="tabular"/>
    </outputs>

    <tests>
        <test>
            <param name="input" value="test_input.fasta"/>
            <output name="output_longestORF" file="test_output.fasta"/>
            <output name="output_ORFs" file="test_output.tab"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool identifies the longest Open Reading Frames within the six-frame translations of a set of sequences. 

**Input**

It takes an amino acid fasta file with all open reading frames (+ and - strand) listed by the correspondng transcript. The tool is designed to process the output of the Galaxy tool "getorf" from the EMBOSS package.

**Output**

For each transcript, the respected longest ORF is identified and listed in fasta format. Furthermore, table with information about seqID, start, end, length, orientation, longest for all ORFs is given.]]>
    </help>
</tool>