<tool id="edu.tamu.cpt.gff.gff2gb" name="GFF3 to GenBank" version="4.0">
    <description>convert gff3 to GenBank</description>
    <macros>
        <import>macros.xml</import>
        <import>cpt-macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
@GENOME_SELECTOR_PRE@

'python $__tool_directory__/gff2gb.py'
@INPUT_GFF@
@INPUT_FASTA@
--transltbl '$transltbl'
> '$output']]></command>
    <inputs>
        <expand macro="input/gff3+fasta"/>
        <param label="Translation Table" name="transltbl" type="select">
            <option value="1">1. The Standard Code</option>
            <option value="2">2. The Vertebrate Mitochondrial Code</option>
            <option value="3">3. The Yeast Mitochondrial Code</option>
            <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
            <option value="5">5. The Invertebrate Mitochondrial Code</option>
            <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
            <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option>
            <option value="10">10. The Euplotid Nuclear Code</option>
            <option value="11" selected="true">11. The Bacterial, Archaeal and Plant Plastid Code</option>
            <option value="12">12. The Alternative Yeast Nuclear Code</option>
            <option value="13">13. The Ascidian Mitochondrial Code</option>
            <option value="14">14. The Alternative Flatworm Mitochondrial Code</option>
            <option value="16">16. Chlorophycean Mitochondrial Code</option>
            <option value="21">21. Trematode Mitochondrial Code</option>
            <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option>
            <option value="23">23. Thraustochytrium Mitochondrial Code</option>
            <option value="24">24. Pterobranchia Mitochondrial Code</option>
            <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
        </param>
    </inputs>
    <outputs>
        <data format="genbank" hidden="false" name="output" label="${gff3_data.name} as GenBank"/>
    </outputs>
    <tests>
        <!-- There have been issues running the diffs for the files -->
        <!-- Going to use asserts and run ONE (or no) diffs -->
        <test>
            <!-- ORIGINAL TEST FILE, regenerated 10.12.2020 -->
            <param name="reference_genome_source" value="history"/>
            <param name="genome_fasta" value="miro.fa"/>
            <param name="gff3_data" value="miro.gff3"/>
            <output name="output" file="miro_from_tool.gbk" compare="sim_size" delta_frac="0.05">
                <assert_contents>
                    <has_text text="RBS"/>
                    <has_text text="gene"/>
                    <has_text text="CDS"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: warningmark

This is a LOSSY conversion. This tool **TRUNCATES** genbank file identifiers if
they are too long. Your data may not "match up" after processing through this
tool.

**What it does**:

Convert gff3 data to genbank. There are many WebApollo specific conventions. A re-numbering is also done.

**Supported / Expected Data**

- gene / mRNA / (CDS, Exon)
- gene / tRNA
- terminator

]]></help>
    <expand macro="citations"/>
</tool>