<tool id="bp_genbank2gff3" name="Genbank to GFF3" version="1.1">
  <description>converter</description>
  <macros>
      <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="stdio" />
  <command><![CDATA[
bp_genbank2gff3.pl
$noinfer
#if str($sofile.sofile) != "__none__":
    --sofile
    #if str($sofile.sofile) == "url":
        "${sofile.so_url}"
    #else:
        live
    #end if
#end if
--outdir -
--ethresh $ethresh
$model
--typesource "${typesource}"

$genbank
> $gff3]]></command>
  <inputs>
    <param label="Genbank file" name="genbank" type="data" format="genbank"/>
    <param name="noinfer" truevalue="" falsevalue="--noinfer" checked="true" type="boolean" label="Infer exon/mRNA subfeatures"/>
    <conditional name="sofile" label="Sequence Ontology">
        <param name="sofile" label="Sequence Ontology File" type="select">
            <option value="__none__" selected="True">None specified</option>
            <option value="live">Latest Sequence Ontology</option>
            <option value="url">User Specified</option>
        </param>
        <when value="__none__" />
        <when value="live" />
        <when value="url">
            <param name="so_url" label="Sequence Ontology URL" type="text"/>
        </when>
    </conditional>
    <param name="ethresh" label="Error threshold for unflattener" type="select">
        <option value="0">Strict</option>
        <option value="1" selected="True">Medium</option>
        <option value="2">Loose</option>
        <option value="3">Ignore Errors</option>
    </param>
    <param name="model" label="Gene Model" type="select">
        <option value="--CDS" selected="True">Default GFF gene model</option>
        <option value="--noCDS">Alternate gene-RNA-protein-exon model</option>
    </param>
    <param name="typesource" label="Sequence Ontology type for landmark feature" help="E.g. chromosome, region, contig" value="contig" type="text" />
  </inputs>
  <outputs>
    <data format="gff3" name="gff3" label="${genbank.name} as GFF3"/>
  </outputs>
  <tests>
      <test>
          <param name="genbank" value="seq.gb" />
          <param name="noinfer" value="True" />
          <output name="gff3" file="seq.gb.0.gff" ftype="gff3" lines_diff="6"/>
      </test>
      <test>
          <param name="genbank" value="seq.gb" />
          <output name="gff3" file="seq.gb.1.gff" ftype="gff3" lines_diff="4"/>
      </test>
  </tests>
  <help><![CDATA[
**What it does**:

This tool uses Bio::SeqFeature::Tools::Unflattener and
Bio::Tools::GFF to convert GenBank flatfiles to GFF3 with gene
containment hierarchies mapped for optimal display in gbrowse.

The input files are assumed to be gzipped GenBank flatfiles for refseq
contigs. The files may contain multiple GenBank records.

**Designed for RefSeq**

This script is designed for RefSeq genomic sequence entries.  It may
work for third party annotations but this has not been tested.
But see below, Uniprot/Swissprot works, EMBL and possibly EMBL/Ensembl
if you don't mind some gene model unflattener errors (dgg).

**G-R-P-E Gene Model**

Don Gilbert worked this over with needs to produce GFF3 suited to
loading to GMOD Chado databases.

This writes GFF with an alternate, but useful Gene model,
instead of the consensus model for GFF3

  [ gene > mRNA> (exon,CDS,UTR) ]

This alternate is

  gene > mRNA > polypeptide > exon

means the only feature with dna bases is the exon.  The others
specify only location ranges on a genome. Exon of course is a child
of mRNA and protein/peptide.

The protein/polypeptide feature is an important one, having all the
annotations of the GenBank CDS feature, protein ID, translation, GO
terms, Dbxrefs to other proteins.

UTRs, introns, CDS-exons are all inferred from the primary exon bases
inside/outside appropriate higher feature ranges.  Other special gene
model features remain the same.

**Authors**

Sheldon McKay (mckays@cshl.edu)

Copyright (c) 2004 Cold Spring Harbor Laboratory.

**Author of hacks for GFF2Chado loading**

Don Gilbert (gilbertd@indiana.edu)
      ]]></help>
  <citations>
    <citation type="doi">10.1101/gr.361602</citation>
  </citations>
</tool>