Mercurial > repos > vipints > fml_gff3togtf
view fml_gff_converter_programs/galaxy/bed_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_bed2gff" name="BED_to_GFF3" version="1.0.0"> <description>converter</description> <command interpreter="python">bed_to_gff3_converter.py $inf_bed > $gff_format </command> <inputs> <param format="bed" name="inf_bed" type="data" label="Convert this query" help="Please look at About format section."/> </inputs> <outputs> <data format="gff3" name="gff_format" /> </outputs> <tests> <test> <param name="inf_bed" value="ccds_genes.bed" /> <output name="gff_format" file="ccds_genes.gff3" /> </test> <test> <param name="inf_bed" value="hs_2009.bed" /> <output name="gff_format" file="hs_2009.gff3" /> </test> </tests> <help> **What it does** This tool converts data from a 12 column UCSC wiggle BED format to GFF3 format. -------- **Example** - The following data in UCSC Wiggle BED format:: chr1 11873 14409 uc001aaa.3 0 + 11873 11873 0 3 354,109,1189, 0,739,1347, - Will be converted to GFF3 format:: ##gff-version 3 chr1 bed2gff gene 11874 14409 0 + . ID=Gene:uc001aaa.3;Name=Gene:uc001aaa.3 chr1 bed2gff transcript 11874 14409 0 + . ID=uc001aaa.3;Name=uc001aaa.3;Parent=Gene:uc001aaa.3 chr1 bed2gff exon 11874 12227 0 + . Parent=uc001aaa.3 chr1 bed2gff exon 12613 12721 0 + . Parent=uc001aaa.3 chr1 bed2gff exon 13221 14409 0 + . Parent=uc001aaa.3 -------- **About formats** **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: The first three BED fields (required) are:: 1. chrom - The name of the chromosome (e.g. chr1, chrY_random). 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.) 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval). The additional BED fields (optional) are:: 4. name - The name of the BED line. 5. score - A score between 0 and 1000. 6. strand - Defines the strand - either '+' or '-'. 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser. 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser. 9. reserved - This should always be set to zero. 10. blockCount - The number of blocks (exons) in the BED line. 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount. 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. **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 or contig. 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>