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comparison gff_to_gtf.xml @ 5:6e589f267c14

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author devteam
date Tue, 04 Nov 2014 12:15:19 -0500
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1 <tool id="fml_gff2gtf" name="GFF-to-GTF" version="2.0.0">
2 <description>converter</description>
3 <command interpreter="python">gff_to_gtf.py $inf_gff3 &gt; $gtf_format
4 </command>
5 <inputs>
6 <param format="gff3,gff" name="inf_gff3" type="data" label="Convert this query" help="Provide genome annotation file in GFF or GFF3."/>
7 </inputs>
8 <outputs>
9 <data format="gtf" name="gtf_format" label="${tool.name} on ${on_string}: Converted" />
10 </outputs>
11 <tests>
12 <test>
13 <param name="inf_gff3" value="AceView_ncbi_37.gff3" />
14 <output name="gtf_format" file="AceView_gff3_to_gtf.gtf" />
15 </test>
16 <test>
17 <param name="inf_gff3" value="ENSEMBL_mm9.gff3" />
18 <output name="gtf_format" file="ENSEMBL_mm9_gff3_to_gtf.gtf" />
19 </test>
20 </tests>
21 <help>
22
23 **What it does**
24
25 This tool converts data from GFF3 to GTF file format (scroll down for format description).
26
27 --------
28
29 **Example**
30
31 - The following data in GFF3 format::
32
33 ##gff-version 3
34 17 protein_coding gene 7255208 7258258 . + . ID=ENSG00000213859;Name=KCTD11
35 17 protein_coding mRNA 7255208 7258258 . + . ID=ENST00000333751;Name=KCTD11-001;Parent=ENSG00000213859
36 17 protein_coding protein 7256262 7256960 . + . ID=ENSP00000328352;Name=KCTD11-001;Parent=ENST00000333751
37 17 protein_coding five_prime_UTR 7255208 7256261 . + . Parent=ENST00000333751
38 17 protein_coding CDS 7256262 7256960 . + 0 Name=CDS:KCTD11;Parent=ENST00000333751,ENSP00000328352
39 17 protein_coding three_prime_UTR 7256961 7258258 . + . Parent=ENST00000333751
40 17 protein_coding exon 7255208 7258258 . + . Parent=ENST00000333751
41
42 - Will be converted to GTF format::
43
44 17 protein_coding exon 7255208 7258258 . + . gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001";
45 17 protein_coding CDS 7256262 7256957 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001"; protein_id "ENSP00000328352";
46 17 protein_coding start_codon 7256262 7256264 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001";
47 17 protein_coding stop_codon 7256958 7256960 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001";
48
49 --------
50
51 **About formats**
52
53
54 **GFF3 format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF3 lines have nine tab-separated fields::
55
56 1. seqid - Must be a chromosome or scaffold.
57 2. source - The program that generated this feature.
58 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon".
59 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
60 5. stop - The ending position of the feature (inclusive).
61 6. score - A score between 0 and 1000. If there is no score value, enter ".".
62 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
63 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 '.'.
64 9. attributes - All lines with the same group are linked together into a single item.
65
66
67 **GTF format** Gene Transfer Format, it borrows from GFF, but has additional structure that warrants a separate definition and format name. GTF lines have nine tab-seaparated fields::
68
69 1. seqname - The name of the sequence.
70 2. source - This indicating where the annotation came from.
71 3. feature - The name of the feature types. The following feature types are required: 'CDS', 'start_codon' and 'stop_codon'
72 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
73 5. end - The ending position of the feature (inclusive).
74 6. score - The score field indicates a degree of confidence in the feature's existence and coordinates.
75 7. strand - Valid entries include '+', '-', or '.'
76 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.
77 9. attributes - These attributes are designed for handling multiple transcripts from the same genomic region.
78
79 --------
80
81 **Copyright**
82
83 2009-2014 Max Planck Society, University of Tübingen &amp; Memorial Sloan Kettering Cancer Center
84
85 Sreedharan VT, Schultheiss SJ, Jean G, Kahles A, Bohnert R, Drewe P, Mudrakarta P, Görnitz N, Zeller G, Rätsch G. Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. Bioinformatics 10.1093/bioinformatics/btt731 (2014)
86
87 </help>
88 </tool>