annotate gff_to_gtf.xml @ 11:5c6f33e20fcc default tip

requirement tag added

<tool id="fml_gff2gtf" name="GFF-to-GTF" version="2.1.0">
	<description>converter</description> 
	<command interpreter="python">gff_to_gtf.py $inf_gff3 &gt; $gtf_format
	</command> 
	<inputs>
  		<param format="gff3,gff" name="inf_gff3" type="data" label="Convert this query" help="Provide genome annotation file in GFF or GFF3."/>
    </inputs>
  	<outputs>
  		<data format="gtf" name="gtf_format" label="${tool.name} on ${on_string}: Converted" /> 
  	</outputs>
	<tests>
        <test>
            <param name="inf_gff3" value="ens_mm9_chr18.gff3" />
            <output name="gtf_format" file="ens_mm9_chr18.gtf" />
        </test>
    </tests>
  	<help>

**What it does**

This tool converts data from GFF to GTF file format (scroll down for format description).

--------

**Example**

- The following data in GFF3::

	##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

- Will be converted to GTF::

	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";

--------

**Reference**

**GFF-to-GTF** is part of oqtans package and cited as [1]_.

.. [1] Sreedharan VT, Schultheiss SJ, Jean G et.al., Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. Bioinformatics (2014). `10.1093/bioinformatics/btt731`_

.. _10.1093/bioinformatics/btt731: http://goo.gl/I75poH

--------

**About formats**

**GFF format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF 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.

**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.

--------

**Copyright**

GFF-to-GTF Wrapper Version 0.6 (Apr 2015)

2009-2015 Max Planck Society, University of Tübingen &amp; Memorial Sloan Kettering Cancer Center

	</help>
</tool>