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/tools/filters/gff2bed.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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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 dataset"/>
 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
29This tool converts data from GFF format to BED format (scroll down for format description).
30
31--------
32
33**Example**
34
35The following data in GFF format::
36
37    chr22  GeneA  enhancer  10000000  10001000  500	 +   .  TGA
38    chr22  GeneA  promoter  10010000  10010100  900	 +   .  TGA
39
40Will 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
53The 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
59The 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>