/tools/filters/bed2gff.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 89 lines · 68 code · 21 blank · 0 comment · 0 complexity · df95bb428aa79fc767eeefe9cae46265 MD5 · raw file
- <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 dataset"/>
- </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>