Mercurial > repos > vipints > fml_gff3togtf

comparison gff_to_bed.xml @ 10:c42c69aa81f8

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo
author vipints <vipin@cbio.mskcc.org>
date Thu, 23 Apr 2015 18:01:45 -0400
parents
children
comparison
equal deleted inserted replaced
9:7d67331368f3 10:c42c69aa81f8
1 <tool id="fml_gff2bed" name="GFF-to-BED" version="2.1.0">
2 <description>converter</description>
3 <command interpreter="python">gff_to_bed.py $inf_gff &gt; $bed_format
4 </command>
5 <inputs>
6 <param format="gtf,gff,gff3" name="inf_gff" type="data" label="Convert this query" help="Provide genome annotation file in GFF, GTF, GFF3."/>
7 </inputs>
8 <outputs>
9 <data format="bed" name="bed_format" label="${tool.name} on ${on_string}: Converted" />
10 </outputs>
11 <tests>
12 <test>
13 <param name="inf_gff" value="MB7_3R.gff3" />
14 <output name="bed_format" file="MB7_3R.bed" />
15 </test>
16 </tests>
17 <help>
18
19 **What it does**
20
21 This tool converts gene transcript annotation from GTF or GFF or GFF3 to UCSC wiggle 12 column BED format.
22
23 --------
24
25 **Example**
26
27 - The following data in GFF3::
28
29 ##gff-version 3
30 chr1 protein_coding gene 11874 14409 0 + . ID=Gene:uc001aaa.3;Name=Gene:uc001aaa.3
31 chr1 protein_coding transcript 11874 14409 0 + . ID=uc001aaa.3;Name=uc001aaa.3;Parent=Gene:uc001aaa.3
32 chr1 protein_coding exon 11874 12227 0 + . Parent=uc001aaa.3
33 chr1 protein_coding exon 12613 12721 0 + . Parent=uc001aaa.3
34 chr1 protein_coding exon 13221 14409 0 + . Parent=uc001aaa.3
35
36 - Will be converted to UCSC Wiggle BED format::
37
38 chr1 11874 14409 uc001aaa.3 0 + 11874 14409 0 3 354,109,1189, 0,739,1347,
39
40 --------
41
42 **Reference**
43
44 **GFF-to-BED** is part of oqtans package and cited as [1]_.
45
46 .. [1] Sreedharan VT, Schultheiss SJ, Jean G et.al., Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. Bioinformatics (2014). `10.1093/bioinformatics/btt731`_
47
48 .. _10.1093/bioinformatics/btt731: http://goo.gl/I75poH
49
50 --------
51
52 **About file formats**
53
54 **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::
55
56
57 1. seqid - Must be a chromosome or scaffold or contig.
58 2. source - The program that generated this feature.
59 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon".
60 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
61 5. stop - The ending position of the feature (inclusive).
62 6. score - A score between 0 and 1000. If there is no score value, enter ".".
63 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
64 8. phase - 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 '.'.
65 9. attributes - All lines with the same group are linked together into a single item.
66
67 **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:
68
69 The first three BED fields (required) are::
70
71 1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
72 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
73 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
74
75 The additional BED fields (optional) are::
76
77 4. name - The name of the BED line.
78 5. score - A score between 0 and 1000.
79 6. strand - Defines the strand - either '+' or '-'.
80 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
81 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
82 9. reserved - This should always be set to zero.
83 10. blockCount - The number of blocks (exons) in the BED line.
84 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
85 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.
86
87 --------
88
89 **Copyright**
90
91 GFF-to-BED Wrapper Version 0.6 (Apr 2015)
92
93 2009-2015 Max Planck Society, University of Tübingen &amp; Memorial Sloan Kettering Cancer Center
94
95 </help>
96 </tool>