Mercurial > repos > vipints > fml_gff3togtf
annotate GFFtools-GX/gff_to_gtf.xml @ 3:ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
author | vipints |
---|---|
date | Wed, 11 Jun 2014 16:29:25 -0400 |
parents | |
children |
rev | line source |
---|---|
3
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
1 <tool id="fml_gff2gtf" name="GFF-to-GTF" version="2.0.0"> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
2 <description>converter</description> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
3 <command interpreter="python">gff_to_gtf.py $inf_gff3 > $gtf_format |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
4 </command> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
5 <inputs> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
6 <param format="gff3,gff" name="inf_gff3" type="data" label="Convert this query" help="Provide genome annotation file in GFF or GFF3."/> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
7 </inputs> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
8 <outputs> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
9 <data format="gtf" name="gtf_format" label="${tool.name} on ${on_string}: Converted" /> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
10 </outputs> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
11 <tests> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
12 <test> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
13 <param name="inf_gff3" value="AceView_ncbi_37.gff3" /> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
14 <output name="gtf_format" file="AceView_gff3_to_gtf.gtf" /> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
15 </test> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
16 <test> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
17 <param name="inf_gff3" value="ENSEMBL_mm9.gff3" /> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
18 <output name="gtf_format" file="ENSEMBL_mm9_gff3_to_gtf.gtf" /> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
19 </test> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
20 </tests> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
21 <help> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
22 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
23 **What it does** |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
24 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
25 This tool converts data from GFF3 to GTF file format (scroll down for format description). |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
26 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
27 -------- |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
28 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
29 **Example** |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
30 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
31 - The following data in GFF3 format:: |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
32 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
33 ##gff-version 3 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
34 17 protein_coding gene 7255208 7258258 . + . ID=ENSG00000213859;Name=KCTD11 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
35 17 protein_coding mRNA 7255208 7258258 . + . ID=ENST00000333751;Name=KCTD11-001;Parent=ENSG00000213859 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
36 17 protein_coding protein 7256262 7256960 . + . ID=ENSP00000328352;Name=KCTD11-001;Parent=ENST00000333751 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
37 17 protein_coding five_prime_UTR 7255208 7256261 . + . Parent=ENST00000333751 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
38 17 protein_coding CDS 7256262 7256960 . + 0 Name=CDS:KCTD11;Parent=ENST00000333751,ENSP00000328352 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
39 17 protein_coding three_prime_UTR 7256961 7258258 . + . Parent=ENST00000333751 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
40 17 protein_coding exon 7255208 7258258 . + . Parent=ENST00000333751 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
41 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
42 - Will be converted to GTF format:: |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
43 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
44 17 protein_coding exon 7255208 7258258 . + . gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001"; |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
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"; |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
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"; |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
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"; |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
48 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
49 -------- |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
50 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
51 **About formats** |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
52 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
53 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
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:: |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
55 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
56 1. seqid - Must be a chromosome or scaffold. |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
57 2. source - The program that generated this feature. |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
58 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon". |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
59 4. start - The starting position of the feature in the sequence. The first base is numbered 1. |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
60 5. stop - The ending position of the feature (inclusive). |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
61 6. score - A score between 0 and 1000. If there is no score value, enter ".". |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
62 7. strand - Valid entries include '+', '-', or '.' (for don't know/care). |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
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 '.'. |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
64 9. attributes - All lines with the same group are linked together into a single item. |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
65 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
66 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
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:: |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
68 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
69 1. seqname - The name of the sequence. |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
70 2. source - This indicating where the annotation came from. |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
71 3. feature - The name of the feature types. The following feature types are required: 'CDS', 'start_codon' and 'stop_codon' |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
72 4. start - The starting position of the feature in the sequence. The first base is numbered 1. |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
73 5. end - The ending position of the feature (inclusive). |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
74 6. score - The score field indicates a degree of confidence in the feature's existence and coordinates. |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
75 7. strand - Valid entries include '+', '-', or '.' |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
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. |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
77 9. attributes - These attributes are designed for handling multiple transcripts from the same genomic region. |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
78 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
79 -------- |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
80 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
81 **Copyright** |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
82 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
83 2009-2014 Max Planck Society, University of Tübingen & Memorial Sloan Kettering Cancer Center |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
84 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
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) |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
86 |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
87 </help> |
ff2c2e6f4ab3
Uploaded version 2.0.0 of gfftools ready to import to local instance
vipints
parents:
diff
changeset
|
88 </tool> |