root/galaxy-central/tools/filters/gff2bed.xml

リビジョン 2, 3.8 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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  </tests>
20  <help>
21
22**What it does**
23
24This tool converts data from GFF format to BED format (scroll down for format description).
25
26--------
27
28**Example**
29
30The following data in GFF format::
31
32    chr22  GeneA  enhancer  10000000  10001000  500      +   .  TGA
33    chr22  GeneA  promoter  10010000  10010100  900      +   .  TGA
34
35Will be converted to BED (**note** that 1 is subtracted from the start coordinate)::
36
37    chr22   9999999  10001000   enhancer   0   +
38    chr22  10009999  10010100   promoter   0   +
39
40------
41
42.. class:: infomark
43
44**About formats**
45
46**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:
47
48The first three BED fields (required) are::
49
50    1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
51    2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
52    3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
53
54The additional BED fields (optional) are::
55
56    4. name - The name of the BED line.
57    5. score - A score between 0 and 1000.
58    6. strand - Defines the strand - either '+' or '-'.
59    7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
60    8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
61    9. reserved - This should always be set to zero.
62   10. blockCount - The number of blocks (exons) in the BED line.
63   11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
64   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.
65   13. expCount - The number of experiments.
66   14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
67   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.
68
69**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::
70
71    1. seqname - Must be a chromosome or scaffold.
72    2. source - The program that generated this feature.
73    3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
74    4. start - The starting position of the feature in the sequence. The first base is numbered 1.
75    5. end - The ending position of the feature (inclusive).
76    6. score - A score between 0 and 1000. If there is no score value, enter ".".
77    7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
78    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 '.'.
79    9. group - All lines with the same group are linked together into a single item.
80
81</help>
82</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。