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1 <tool id="gff2bed1" name="GFF-to-BED" version="1.0.1">
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2 <description>converter</description>
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3 <command interpreter="python">gff_to_bed_converter.py $input $out_file1</command>
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4 <inputs>
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5 <param format="gff" 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="bed" 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="5.gff" ftype="gff"/>
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13 <output name="out_file1" file="gff2bed_out.bed"/>
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14 </test>
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15 <test>
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16 <param name="input" value="gff2bed_in2.gff" ftype="gff"/>
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17 <output name="out_file1" file="gff2bed_out2.bed"/>
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18 </test>
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19 <test>
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20 <!-- Test conversion of gff3 file. -->
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21 <param name="input" value="5.gff3" ftype="gff"/>
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22 <output name="out_file1" file="gff2bed_out3.bed"/>
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23 </test>
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24 </tests>
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25 <help>
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26
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27 **What it does**
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28
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29 This tool converts data from GFF format to BED format (scroll down for format description).
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30
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31 --------
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32
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33 **Example**
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34
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35 The following data in GFF format::
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36
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37 chr22 GeneA enhancer 10000000 10001000 500 + . TGA
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38 chr22 GeneA promoter 10010000 10010100 900 + . TGA
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39
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40 Will be converted to BED (**note** that 1 is subtracted from the start coordinate)::
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41
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42 chr22 9999999 10001000 enhancer 0 +
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43 chr22 10009999 10010100 promoter 0 +
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44
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45 ------
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46
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47 .. class:: infomark
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48
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49 **About formats**
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50
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51 **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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52
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53 The first three BED fields (required) are::
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54
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55 1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
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56 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
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57 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
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58
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59 The additional BED fields (optional) are::
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60
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61 4. name - The name of the BED line.
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62 5. score - A score between 0 and 1000.
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63 6. strand - Defines the strand - either '+' or '-'.
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64 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
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65 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
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66 9. reserved - This should always be set to zero.
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67 10. blockCount - The number of blocks (exons) in the BED line.
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68 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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69 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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70 13. expCount - The number of experiments.
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71 14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
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72 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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73
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74 **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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75
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76 1. seqname - Must be a chromosome or scaffold.
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77 2. source - The program that generated this feature.
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78 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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79 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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80 5. end - The ending position of the feature (inclusive).
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81 6. score - A score between 0 and 1000. If there is no score value, enter ".".
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82 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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83 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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84 9. group - All lines with the same group are linked together into a single item.
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85
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86 </help>
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87 </tool>
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