root/galaxy-central/tools/filters/bed2gff.xml

<tool id="bed2gff1" name="BED-to-GFF" version="2.0.0">
  <description>converter</description>
  <command interpreter="python">bed_to_gff_converter.py $input $out_file1</command>
  <inputs>
    <param format="bed" name="input" type="data" label="Convert this query"/>
  </inputs>
  <outputs>
    <data format="gff" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input" value="9.bed"/>
      <output name="out_file1" file="bed2gff_out.gff"/>
    </test>
  </tests>
  <help>

**What it does**

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

--------

**Example**

The following data in BED format::

        chr28   346187  388197  BC114771        0       +       346187  388197  0       9       144,81,115,63,155,96,134,105,112,       0,24095,26190,31006,32131,33534,36994,41793,41898,

Will be converted to GFF (**note** that the start coordinate is incremented by 1)::

        ##gff-version 2
        ##bed_to_gff_converter.py

        chr28   bed2gff mRNA    346188  388197  0       +       .       mRNA BC114771;
        chr28   bed2gff exon    346188  346331  0       +       .       exon BC114771;
        chr28   bed2gff exon    370283  370363  0       +       .       exon BC114771;
        chr28   bed2gff exon    372378  372492  0       +       .       exon BC114771;
        chr28   bed2gff exon    377194  377256  0       +       .       exon BC114771;
        chr28   bed2gff exon    378319  378473  0       +       .       exon BC114771;
        chr28   bed2gff exon    379722  379817  0       +       .       exon BC114771;
        chr28   bed2gff exon    383182  383315  0       +       .       exon BC114771;
        chr28   bed2gff exon    387981  388085  0       +       .       exon BC114771;
        chr28   bed2gff exon    388086  388197  0       +       .       exon BC114771;


------

.. class:: informark

**About 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.
   13. expCount - The number of experiments.
   14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
   15. expScores - A comma-separated list of experiment scores. All of the expScores should be relative to expIds. The number of items in this list should correspond to expCount.

**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. seqname - Must be a chromosome or scaffold.
    2. source - The program that generated this feature.
    3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
    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 - 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. 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. If the feature is not a coding exon, the value should be '.'.
    9. group - All lines with the same group are linked together into a single item.

</help>
</tool>