tool.xml

<tool id="barcode_validator" name="Barcode Validator" version="1.0.0">
    <description>Structural validation of DNA barcode sequences</description>
    <requirements>
        <requirement type="package" version="1.81">biopython</requirement>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/structural_validator.py'
            --marker '$marker'
            --kingdom '$kingdom'
            --taxon '$taxon'
            --fasta '$input'
            > '$output'
    ]]></command>

    <inputs>
        <param name="marker" type="select" label="DNA Barcode Marker">
            <option value="COI-5P">COI-5P</option>
            <option value="matK">matK</option>
            <option value="rbcL">rbcL</option>
            <option value="ITS1">ITS1</option>
            <option value="ITS2">ITS2</option>
            <option value="16S">16S</option>
            <option value="18S">18S</option>
        </param>

        <param name="kingdom" type="select" label="Kingdom">
            <option value="Animalia">Animalia</option>
            <option value="Plantae">Plantae</option>
            <option value="Fungi">Fungi</option>
            <option value="Bacteria">Bacteria</option>
            <option value="Archaea">Archaea</option>
        </param>

        <param name="taxon" type="text" label="Taxon Name" help="Taxon name assigned to the specimen">
            <validator type="empty_field" />
        </param>

        <param name="input" type="data" format="fasta" label="Input FASTA" />
    </inputs>

    <outputs>
        <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
    </outputs>

    <tests>
        <test>
            <param name="marker" value="COI-5P" />
            <param name="kingdom" value="Animalia" />
            <param name="taxon" value="Homo sapiens" />
            <param name="input" value="test.fa" />
            <output name="output">
                <assert_contents>
                    <has_line_matching expression="^sequence_id\ttranslation_table\thas_stop_codons\tstop_codon_positions" />
                </assert_contents>
            </output>
        </test>
    </tests>

    <help><![CDATA[
**What it does**

This tool validates DNA barcode sequences as follows:

* If it's a coding marker (COI-5P, matK, rbcL): resolve the taxonomic name against NCBI taxonomy to obtain Phylum,
  Class and Family; determine genetic code based on taxonomy and marker; align the sequence against the appropriate
  HMM to determine phase; translate to amino acids to check for premature stop codons that might indicate pseudogenes.
* In all cases: count the number of ambiguous bases (i.e. non ACGT- characters) within and outside the marker region;
  count the sequence length within and outside the marker region.

The tool outputs a TSV file with at least the following columns:

* ambig_basecount: number of ambiguous bases
* ambig_full_basecount: number of ambiguous bases including outside the marker region
* error: error message if any
* identification: taxonomic identification as provided
* nuc_basecount: number of nucleotides
* nuc_full_basecount: number of nucleotides including outside the marker region
* sequence_id: ID from the FASTA file
* stop_codons: number of stop codons found

In addition, there may be other columns, emitted in any order (but with unique headings).

**Input**

* DNA Barcode Marker: Select the marker gene being analyzed
* Kingdom: Select the kingdom the organism belongs to
* Taxon Name: Enter the taxonomic name assigned to the specimen
* Input FASTA: File containing sequence to validate

**Output**

A tabular (TSV) file containing validation results for the sequence.
    ]]></help>

    <citations>
        <citation type="doi">10.1093/nar/gkf436</citation>  <!-- Biopython -->
        <citation type="doi">10.1093/nar/gkx1000</citation>  <!-- NCBI Taxonomy -->
    </citations>

</tool>