<tool id="fml_gtf2gff3" name="GTF_to_GFF3" version="1.0.0">
	<description>converter</description> 
	<command interpreter="python">gtf_to_gff3_converter.py $inf_gtf > $gff3_format 
	</command> 
	<inputs>
  		<param format="gtf" name="inf_gtf" type="data" label="File in GTF format" help="GTF file for converting to GFF3 format."/>
        </inputs>
  	<outputs>
  		<data format="gff3" name="gff3_format" /> 
  	</outputs>
	    <tests>
        	<test>
                <param name="inf_gtf" value="UCSC_transcripts.gtf" />
                <output name="gff3_format" file="UCSC_transcripts.gff3" />
        	</test>
        	<test>
                <param name="inf_gtf" value="JGI_genes.gtf" />
                <output name="gff3_format" file="JGI_genes.gff3" />
        	</test>
        	<test>
                <param name="inf_gtf" value="ENSEMBL_mm9.gtf" />
                <output name="gff3_format" file="ENSEMBL_mm9.gff3" />
        	</test>
        	<test>
                <param name="inf_gtf" value="AceView_ncbi_37.gtf" />
                <output name="gff3_format" file="AceView_ncbi_37.gff3" />
        	</test>
        </tests>
  	<help>

**What it does**

This tool converts data from GTF format to valid GFF3 format.

--------

**Example**

- The following data in GTF format::

	17      protein_coding  exon    7255208 7258258 .       +       .        gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001";
	17      protein_coding  CDS     7256262 7256957 .       +       0        gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001"; protein_id "ENSP00000328352";
	17      protein_coding  start_codon     7256262 7256264 .       +       0        gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001";
	17      protein_coding  stop_codon      7256958 7256960 .       +       0        gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001";

- Will be converted to GFF3 format::

	##gff-version 3
	17      protein_coding  gene    7255208 7258258 .       +       .       ID=ENSG00000213859;Name=KCTD11
	17      protein_coding  mRNA    7255208 7258258 .       +       .       ID=ENST00000333751;Name=KCTD11-001;Parent=ENSG00000213859
	17      protein_coding  protein 7256262 7256960 .       +       .       ID=ENSP00000328352;Name=KCTD11-001;Parent=ENST00000333751
	17      protein_coding  five_prime_UTR  7255208 7256261 .       +       .       Parent=ENST00000333751
	17      protein_coding  CDS     7256262 7256960 .       +       0       Name=CDS:KCTD11;Parent=ENST00000333751,ENSP00000328352
	17      protein_coding  three_prime_UTR 7256961 7258258 .       +       .       Parent=ENST00000333751
	17      protein_coding  exon    7255208 7258258 .       +       .       Parent=ENST00000333751

--------

**About formats**

**GTF format** Gene Transfer Format, it borrows from GFF, but has additional structure that warrants a separate definition and format name. GTF lines have nine tab-seaparated fields:

    1. seqname - The name of the sequence.
    2. source - This indicating where the annotation came from.
    3. feature - The name of the feature types. The following feature types are required: 'CDS', 'start_codon' and 'stop_codon'
    4. start - The starting position of the feature in the sequence. The first base is numbered 1.
    5. end - The ending position of the feature (inclusive).
    6. score - The score field indicates a degree of confidence in the feature's existence and coordinates.
    7. strand - Valid entries include '+', '-', or '.'
    8. frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base.
    9. attributes - These attributes are designed for handling multiple transcripts from the same genomic region.

**GFF3 format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF3 lines have nine tab-separated fields:

    1. seqid - Must be a chromosome or scaffold.
    2. source - The program that generated this feature.
    3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon". 
    4. start - The starting position of the feature in the sequence. The first base is numbered 1.
    5. stop - The ending position of the feature (inclusive).
    6. score - A score between 0 and 1000. If there is no score value, enter ".".
    7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
    8. phase - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'.
    9. attributes - All lines with the same group are linked together into a single item.

--------

This tool is a part of the **MLB Group at Friedrich Miescher Laboratory of the Max Planck Society**. Copyright (C) 2010 Vipin T. Sreedharan (vipin.ts@tuebingen.mpg.de)
	</help>
</tool>