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1 <tool id="bed2gff1" name="BED-to-GFF" version="2.0.0">
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2 <description>converter</description>
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3 <command interpreter="python">bed_to_gff_converter.py $input $out_file1</command>
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4 <inputs>
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5 <param format="bed" name="input" type="data" label="Convert this query"/>
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6 </inputs>
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7 <outputs>
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8 <data format="gff" name="out_file1" />
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9 </outputs>
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10 <tests>
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11 <test>
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12 <param name="input" value="9.bed"/>
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13 <output name="out_file1" file="bed2gff_out.gff"/>
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14 </test>
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15 </tests>
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16 <help>
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17
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18 **What it does**
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19
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20 This tool converts data from BED format to GFF format (scroll down for format description).
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21
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22 --------
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23
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24 **Example**
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25
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26 The following data in BED format::
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27
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28 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,
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29
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30 Will be converted to GFF (**note** that the start coordinate is incremented by 1)::
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31
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32 ##gff-version 2
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33 ##bed_to_gff_converter.py
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34
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35 chr28 bed2gff mRNA 346188 388197 0 + . mRNA BC114771;
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36 chr28 bed2gff exon 346188 346331 0 + . exon BC114771;
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37 chr28 bed2gff exon 370283 370363 0 + . exon BC114771;
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38 chr28 bed2gff exon 372378 372492 0 + . exon BC114771;
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39 chr28 bed2gff exon 377194 377256 0 + . exon BC114771;
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40 chr28 bed2gff exon 378319 378473 0 + . exon BC114771;
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41 chr28 bed2gff exon 379722 379817 0 + . exon BC114771;
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42 chr28 bed2gff exon 383182 383315 0 + . exon BC114771;
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43 chr28 bed2gff exon 387981 388085 0 + . exon BC114771;
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44 chr28 bed2gff exon 388086 388197 0 + . exon BC114771;
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45
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46
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47 ------
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48
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49 .. class:: informark
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50
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51 **About formats**
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52
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53 **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:
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54
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55 The first three BED fields (required) are::
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56
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57 1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
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58 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
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59 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
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60
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61 The additional BED fields (optional) are::
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62
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63 4. name - The name of the BED line.
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64 5. score - A score between 0 and 1000.
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65 6. strand - Defines the strand - either '+' or '-'.
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66 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
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67 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
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68 9. reserved - This should always be set to zero.
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69 10. blockCount - The number of blocks (exons) in the BED line.
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70 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
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71 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.
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72 13. expCount - The number of experiments.
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73 14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
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74 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.
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75
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76 **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::
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77
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78 1. seqname - Must be a chromosome or scaffold.
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79 2. source - The program that generated this feature.
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80 3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
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81 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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82 5. end - The ending position of the feature (inclusive).
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83 6. score - A score between 0 and 1000. If there is no score value, enter ".".
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84 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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85 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 '.'.
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86 9. group - All lines with the same group are linked together into a single item.
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87
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88 </help>
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89 </tool>
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