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comparison tools/filters/gff2bed.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="gff2bed1" name="GFF-to-BED" version="1.0.1">
2 <description>converter</description>
3 <command interpreter="python">gff_to_bed_converter.py $input $out_file1</command>
4 <inputs>
5 <param format="gff" name="input" type="data" label="Convert this query"/>
6 </inputs>
7 <outputs>
8 <data format="bed" name="out_file1" />
9 </outputs>
10 <tests>
11 <test>
12 <param name="input" value="5.gff" ftype="gff"/>
13 <output name="out_file1" file="gff2bed_out.bed"/>
14 </test>
15 <test>
16 <param name="input" value="gff2bed_in2.gff" ftype="gff"/>
17 <output name="out_file1" file="gff2bed_out2.bed"/>
18 </test>
19 <test>
20 <!-- Test conversion of gff3 file. -->
21 <param name="input" value="5.gff3" ftype="gff"/>
22 <output name="out_file1" file="gff2bed_out3.bed"/>
23 </test>
24 </tests>
25 <help>
26
27 **What it does**
28
29 This tool converts data from GFF format to BED format (scroll down for format description).
30
31 --------
32
33 **Example**
34
35 The following data in GFF format::
36
37 chr22 GeneA enhancer 10000000 10001000 500 + . TGA
38 chr22 GeneA promoter 10010000 10010100 900 + . TGA
39
40 Will be converted to BED (**note** that 1 is subtracted from the start coordinate)::
41
42 chr22 9999999 10001000 enhancer 0 +
43 chr22 10009999 10010100 promoter 0 +
44
45 ------
46
47 .. class:: infomark
48
49 **About formats**
50
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:
52
53 The first three BED fields (required) are::
54
55 1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
56 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
57 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
58
59 The additional BED fields (optional) are::
60
61 4. name - The name of the BED line.
62 5. score - A score between 0 and 1000.
63 6. strand - Defines the strand - either '+' or '-'.
64 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
65 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
66 9. reserved - This should always be set to zero.
67 10. blockCount - The number of blocks (exons) in the BED line.
68 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
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.
70 13. expCount - The number of experiments.
71 14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
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.
73
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::
75
76 1. seqname - Must be a chromosome or scaffold.
77 2. source - The program that generated this feature.
78 3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
79 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
80 5. end - The ending position of the feature (inclusive).
81 6. score - A score between 0 and 1000. If there is no score value, enter ".".
82 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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 '.'.
84 9. group - All lines with the same group are linked together into a single item.
85
86 </help>
87 </tool>