<tool id="fml_bed2gff" name="BED-to-GFF" version="2.1.0">
	<description>converter</description>
	<command interpreter="python">bed_to_gff.py $inf_bed  &gt; $gff_format 
	</command> 
	<inputs>
  		<param format="bed" name="inf_bed" type="data" label="Convert this query" help="Provide genome annotation in 12 column BED format."/>
    </inputs>
  	<outputs>
  		<data format="gff" name="gff_format" label="${tool.name} on ${on_string}: Converted" /> 
  	</outputs>
	<tests>
        <test>
            <param name="inf_bed" value="CCDS30770.bed" />
            <output name="gff_format" file="CCDS30770.gff" />
        </test>
    </tests>
  	<help>

**What it does**

This tool converts data from a 12 column UCSC wiggle BED format to GFF3 (scroll down for format description).

--------

**Example**

- The following data in UCSC Wiggle BED format::

	chr1    11873   14409   uc001aaa.3      0       +       11873   11873   0       3       354,109,1189,   0,739,1347,

- Will be converted to GFF3::

	##gff-version 3
	chr1    bed2gff gene    11874   14409   0       +       .       ID=Gene:uc001aaa.3;Name=Gene:uc001aaa.3
	chr1    bed2gff transcript      11874   14409   0       +       .       ID=uc001aaa.3;Name=uc001aaa.3;Parent=Gene:uc001aaa.3
	chr1    bed2gff exon    11874   12227   0       +       .       Parent=uc001aaa.3
	chr1    bed2gff exon    12613   12721   0       +       .       Parent=uc001aaa.3
	chr1    bed2gff exon    13221   14409   0       +       .       Parent=uc001aaa.3

--------

**Reference**

**BED-to-GFF** 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 file formats**

**BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several additional optional ones:

The first three BED fields (required) are::

    1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
    2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
    3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).

The additional BED fields (optional) are::

    4. name - The name of the BED line.
    5. score - A score between 0 and 1000.
    6. strand - Defines the strand - either '+' or '-'.
    7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
    8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
    9. reserved - This should always be set to zero.
   10. blockCount - The number of blocks (exons) in the BED line.
   11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
   12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.

**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 or contig.
    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.

--------

**Copyright**

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

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

	</help>
</tool>