<tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.10">
    <description>Gives a codon aware alignment</description>
    <requirements>
        <requirement type="package" version="1.67">biopython</requirement>
    </requirements>
    <version_command>
python $__tool_directory__/align_back_trans.py --version
    </version_command>
    <command detect_errors="aggressive">
python $__tool_directory__/align_back_trans.py $prot_align.ext '$prot_align' '$nuc_file' '$out_nuc_align' '$table'
    </command>
    <inputs>
        <param name="prot_align" type="data" format="fasta,clustal" label="Aligned protein file" help="Mutliple sequence file in FASTA, ClustalW or PHYLIP format." />
        <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons">
            <option value="1">1. Standard</option>
            <option value="2">2. Vertebrate Mitochondrial</option>
            <option value="3">3. Yeast Mitochondrial</option>
            <option value="4">4. Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
            <option value="5">5. Invertebrate Mitochondrial</option>
            <option value="6">6. Ciliate Macronuclear and Dasycladacean</option>
            <option value="9">9. Echinoderm Mitochondrial</option>
            <option value="10">10. Euplotid Nuclear</option>
            <option value="11">11. Bacterial</option>
            <option value="12">12. Alternative Yeast Nuclear</option>
            <option value="13">13. Ascidian Mitochondrial</option>
            <option value="14">14. Flatworm Mitochondrial</option>
            <option value="15">15. Blepharisma Macronuclear</option>
            <option value="16">16. Chlorophycean Mitochondrial</option>
            <option value="21">21. Trematode Mitochondrial</option>
            <option value="22">22. Scenedesmus obliquus</option>
            <option value="23">23. Thraustochytrium Mitochondrial</option>
            <option value="24">24. Pterobranchia Mitochondrial</option>
            <option value="25">25. Candidate Division SR1 and Gracilibacteria</option>
            <!-- TODO, these are not in Biopython 1.67
            <option value="26">26. Pachysolen tannophilus Nuclear</option>
            <option value="26">27. Karyorelict Nuclear</option>
            <option value="26">28. Condylostoma Nuclear</option>
            <option value="26">29. Mesodinium Nuclear</option>
            <option value="26">30. Peritrich Nuclear</option>
            <option value="26">31. Blastocrithidia Nuclear</option>
            -->
            <option value="0">Don't check the translation</option>
        </param>
        <param name="nuc_file" type="data" format="fasta" label="Unaligned nucleotide sequences" help="FASTA format, using same identifiers as your protein alignment" />
    </inputs>
    <outputs>
        <data name="out_nuc_align" format_source="prot_align" metadata_source="prot_align" label="${prot_align.name} (back-translated)"/>
    </outputs>
    <tests>
        <test>
            <param name="prot_align" value="demo_prot_align.fasta" />
            <param name="nuc_file" value="demo_nucs.fasta" />
            <param name="table" value="0" />
            <output name="out_nuc_align" file="demo_nuc_align.fasta" />
        </test>
        <test>
            <param name="prot_align" value="demo_prot_align.fasta" />
            <param name="nuc_file" value="demo_nucs_trailing_stop.fasta" />
            <param name="table" value="11" />
            <output name="out_nuc_align" file="demo_nuc_align.fasta" />
        </test>
    </tests>
    <help>
**What it does**

Takes an input file of aligned protein sequences (typically FASTA or Clustal
format), and a matching file of unaligned nucleotide sequences (FASTA format,
using the same identifiers), and threads the nucleotide sequences onto the
protein alignment to produce a codon aware nucleotide alignment - which can
be viewed as a back translation.

If you specify one of the standard NCBI genetic codes (recommended), then the
translation is verified. This will allow fuzzy matching if stop codons in the
protein sequence have been reprented as X, and will allow for a trailing stop
codon present in the nucleotide sequences but not the protein.

Note - the protein and nucleotide sequences must use the same identifers.

Note - If no translation table is specified, the provided nucleotide sequences
should be exactly three times the length of the protein sequences (exluding the gaps).

Note - the nucleotide FASTA file may contain extra sequences not in the
protein alignment, they will be ignored. This can be useful if for example
you have a nucleotide FASTA file containing all the genes in an organism,
while the protein alignment is for a specific gene family.

**Example**

Given this protein alignment in FASTA format::

    >Alpha
    DEER
    >Beta
    DE-R
    >Gamma
    D--R

and this matching unaligned nucleotide FASTA file::

    >Alpha
    GATGAGGAACGA
    >Beta
    GATGAGCGU
    >Gamma
    GATCGG

the tool would return this nucleotide alignment::

    >Alpha
    GATGAGGAACGA
    >Beta
    GATGAG---CGU
    >Gamma
    GAT------CGG

Notice that all the gaps are multiples of three in length.


**Citation**

This tool uses Biopython, so if you use this Galaxy tool in work leading to a
scientific publication please cite the following paper:

Cock et al (2009). Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.

This tool is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans
    </help>
    <citations>
        <citation type="doi">10.7717/peerj.167</citation>
        <citation type="doi">10.1093/bioinformatics/btp163</citation>
    </citations>
</tool>