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view fml_gff_converter_programs/galaxy/gtf_to_gff3.xml @ 0:ed53dca1c6ff
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | vipints |
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date | Tue, 07 Jun 2011 17:26:20 -0400 |
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<tool id="fml_gtf2gff3" name="GTF_to_GFF3" version="1.0.0"> <description>converter</description> <command interpreter="python">gtf_to_gff3_converter.py $inf_gtf > $gff3_format </command> <inputs> <param format="gtf" name="inf_gtf" type="data" label="File in GTF format" help="GTF file for converting to GFF3 format."/> </inputs> <outputs> <data format="gff3" name="gff3_format" /> </outputs> <tests> <test> <param name="inf_gtf" value="UCSC_transcripts.gtf" /> <output name="gff3_format" file="UCSC_transcripts.gff3" /> </test> <test> <param name="inf_gtf" value="JGI_genes.gtf" /> <output name="gff3_format" file="JGI_genes.gff3" /> </test> <test> <param name="inf_gtf" value="ENSEMBL_mm9.gtf" /> <output name="gff3_format" file="ENSEMBL_mm9.gff3" /> </test> <test> <param name="inf_gtf" value="AceView_ncbi_37.gtf" /> <output name="gff3_format" file="AceView_ncbi_37.gff3" /> </test> </tests> <help> **What it does** This tool converts data from GTF format to valid GFF3 format. -------- **Example** - The following data in GTF format:: 17 protein_coding exon 7255208 7258258 . + . gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001"; 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"; 17 protein_coding start_codon 7256262 7256264 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001"; 17 protein_coding stop_codon 7256958 7256960 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001"; - Will be converted to GFF3 format:: ##gff-version 3 17 protein_coding gene 7255208 7258258 . + . ID=ENSG00000213859;Name=KCTD11 17 protein_coding mRNA 7255208 7258258 . + . ID=ENST00000333751;Name=KCTD11-001;Parent=ENSG00000213859 17 protein_coding protein 7256262 7256960 . + . ID=ENSP00000328352;Name=KCTD11-001;Parent=ENST00000333751 17 protein_coding five_prime_UTR 7255208 7256261 . + . Parent=ENST00000333751 17 protein_coding CDS 7256262 7256960 . + 0 Name=CDS:KCTD11;Parent=ENST00000333751,ENSP00000328352 17 protein_coding three_prime_UTR 7256961 7258258 . + . Parent=ENST00000333751 17 protein_coding exon 7255208 7258258 . + . Parent=ENST00000333751 -------- **About formats** **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: 1. seqname - The name of the sequence. 2. source - This indicating where the annotation came from. 3. feature - The name of the feature types. The following feature types are required: 'CDS', 'start_codon' and 'stop_codon' 4. start - The starting position of the feature in the sequence. The first base is numbered 1. 5. end - The ending position of the feature (inclusive). 6. score - The score field indicates a degree of confidence in the feature's existence and coordinates. 7. strand - Valid entries include '+', '-', or '.' 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. 9. attributes - These attributes are designed for handling multiple transcripts from the same genomic region. **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: 1. seqid - Must be a chromosome or scaffold. 2. source - The program that generated this feature. 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon". 4. start - The starting position of the feature in the sequence. The first base is numbered 1. 5. stop - The ending position of the feature (inclusive). 6. score - A score between 0 and 1000. If there is no score value, enter ".". 7. strand - Valid entries include '+', '-', or '.' (for don't know/care). 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 '.'. 9. attributes - All lines with the same group are linked together into a single item. -------- 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) </help> </tool>