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comparison fml_gff_converter_programs/galaxy/gtf_to_gff3.xml @ 0:ed53dca1c6ff

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author vipints
date Tue, 07 Jun 2011 17:26:20 -0400
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1 <tool id="fml_gtf2gff3" name="GTF_to_GFF3" version="1.0.0">
2 <description>converter</description>
3 <command interpreter="python">gtf_to_gff3_converter.py $inf_gtf > $gff3_format
4 </command>
5 <inputs>
6 <param format="gtf" name="inf_gtf" type="data" label="File in GTF format" help="GTF file for converting to GFF3 format."/>
7 </inputs>
8 <outputs>
9 <data format="gff3" name="gff3_format" />
10 </outputs>
11 <tests>
12 <test>
13 <param name="inf_gtf" value="UCSC_transcripts.gtf" />
14 <output name="gff3_format" file="UCSC_transcripts.gff3" />
15 </test>
16 <test>
17 <param name="inf_gtf" value="JGI_genes.gtf" />
18 <output name="gff3_format" file="JGI_genes.gff3" />
19 </test>
20 <test>
21 <param name="inf_gtf" value="ENSEMBL_mm9.gtf" />
22 <output name="gff3_format" file="ENSEMBL_mm9.gff3" />
23 </test>
24 <test>
25 <param name="inf_gtf" value="AceView_ncbi_37.gtf" />
26 <output name="gff3_format" file="AceView_ncbi_37.gff3" />
27 </test>
28 </tests>
29 <help>
30
31 **What it does**
32
33 This tool converts data from GTF format to valid GFF3 format.
34
35 --------
36
37 **Example**
38
39 - The following data in GTF format::
40
41 17 protein_coding exon 7255208 7258258 . + . gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001";
42 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";
43 17 protein_coding start_codon 7256262 7256264 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001";
44 17 protein_coding stop_codon 7256958 7256960 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001";
45
46 - Will be converted to GFF3 format::
47
48 ##gff-version 3
49 17 protein_coding gene 7255208 7258258 . + . ID=ENSG00000213859;Name=KCTD11
50 17 protein_coding mRNA 7255208 7258258 . + . ID=ENST00000333751;Name=KCTD11-001;Parent=ENSG00000213859
51 17 protein_coding protein 7256262 7256960 . + . ID=ENSP00000328352;Name=KCTD11-001;Parent=ENST00000333751
52 17 protein_coding five_prime_UTR 7255208 7256261 . + . Parent=ENST00000333751
53 17 protein_coding CDS 7256262 7256960 . + 0 Name=CDS:KCTD11;Parent=ENST00000333751,ENSP00000328352
54 17 protein_coding three_prime_UTR 7256961 7258258 . + . Parent=ENST00000333751
55 17 protein_coding exon 7255208 7258258 . + . Parent=ENST00000333751
56
57 --------
58
59 **About formats**
60
61 **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:
62
63 1. seqname - The name of the sequence.
64 2. source - This indicating where the annotation came from.
65 3. feature - The name of the feature types. The following feature types are required: 'CDS', 'start_codon' and 'stop_codon'
66 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
67 5. end - The ending position of the feature (inclusive).
68 6. score - The score field indicates a degree of confidence in the feature's existence and coordinates.
69 7. strand - Valid entries include '+', '-', or '.'
70 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.
71 9. attributes - These attributes are designed for handling multiple transcripts from the same genomic region.
72
73 **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:
74
75 1. seqid - Must be a chromosome or scaffold.
76 2. source - The program that generated this feature.
77 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon".
78 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
79 5. stop - The ending position of the feature (inclusive).
80 6. score - A score between 0 and 1000. If there is no score value, enter ".".
81 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
82 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 '.'.
83 9. attributes - All lines with the same group are linked together into a single item.
84
85 --------
86
87 This tool is a part of the **MLB Group at Friedrich Miescher Laboratory of the Max Planck Society**. Copyright (C) 2010 Vipin T. Sreedharan (vipin.ts@tuebingen.mpg.de)
88 </help>
89 </tool>