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annotate GFFtools-GX/bed_to_gff.xml @ 3:ff2c2e6f4ab3

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Uploaded version 2.0.0 of gfftools ready to import to local instance
author vipints
date Wed, 11 Jun 2014 16:29:25 -0400
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3
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1 <tool id="fml_bed2gff" name="BED-to-GFF" version="2.0.0">
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2 <description>converter</description>
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3 <command interpreter="python">bed_to_gff.py $inf_bed > $gff_format
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4 </command>
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5 <inputs>
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6 <param format="bed" name="inf_bed" type="data" label="Convert this query" help="Provide genome annotation in 12 column BED format."/>
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7 </inputs>
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8 <outputs>
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9 <data format="gff3" name="gff_format" label="${tool.name} on ${on_string}: Converted" />
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10 </outputs>
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11 <tests>
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12 <test>
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13 <param name="inf_bed" value="ccds_genes.bed" />
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14 <output name="gff_format" file="ccds_genes.gff3" />
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15 </test>
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16 <test>
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17 <param name="inf_bed" value="hs_2009.bed" />
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18 <output name="gff_format" file="hs_2009.gff3" />
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19 </test>
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20 </tests>
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21 <help>
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22
ff2c2e6f4ab3 Uploaded version 2.0.0 of gfftools ready to import to local instance
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23 **What it does**
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24
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25 This tool converts data from a 12 column UCSC wiggle BED format to GFF3 (scroll down for format description).
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26
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27 --------
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28
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29 **Example**
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30
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31 - The following data in UCSC Wiggle BED format::
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32
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33 chr1 11873 14409 uc001aaa.3 0 + 11873 11873 0 3 354,109,1189, 0,739,1347,
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34
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35 - Will be converted to GFF3::
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36
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37 ##gff-version 3
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38 chr1 bed2gff gene 11874 14409 0 + . ID=Gene:uc001aaa.3;Name=Gene:uc001aaa.3
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39 chr1 bed2gff transcript 11874 14409 0 + . ID=uc001aaa.3;Name=uc001aaa.3;Parent=Gene:uc001aaa.3
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40 chr1 bed2gff exon 11874 12227 0 + . Parent=uc001aaa.3
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41 chr1 bed2gff exon 12613 12721 0 + . Parent=uc001aaa.3
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42 chr1 bed2gff exon 13221 14409 0 + . Parent=uc001aaa.3
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43
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44 --------
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45
ff2c2e6f4ab3 Uploaded version 2.0.0 of gfftools ready to import to local instance
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46 **About formats**
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47
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48 **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:
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49
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50 The first three BED fields (required) are::
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51
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52 1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
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53 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
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54 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
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55
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56 The additional BED fields (optional) are::
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57
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58 4. name - The name of the BED line.
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59 5. score - A score between 0 and 1000.
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60 6. strand - Defines the strand - either '+' or '-'.
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61 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
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62 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
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63 9. reserved - This should always be set to zero.
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64 10. blockCount - The number of blocks (exons) in the BED line.
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65 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
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66 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.
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67
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68 **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::
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69
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70 1. seqid - Must be a chromosome or scaffold or contig.
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71 2. source - The program that generated this feature.
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72 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon".
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73 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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74 5. stop - The ending position of the feature (inclusive).
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75 6. score - A score between 0 and 1000. If there is no score value, enter ".".
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76 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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77 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 '.'.
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78 9. attributes - All lines with the same group are linked together into a single item.
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79
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80 --------
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81
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82 **Copyright**
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83
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84 2009-2014 Max Planck Society, University of Tübingen &amp; Memorial Sloan Kettering Cancer Center
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85
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86 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)
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87
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88 </help>
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89 </tool>