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1 <tool id="fml_gbk2gff" name="GBK-to-GFF" version="2.0.0">
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2 <description>converter</description>
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3 <command interpreter="python">gbk_to_gff.py $inf_gbk > $gff_format
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4 </command>
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5 <inputs>
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6 <param format="gb,gbk,genbank,txt" name="inf_gbk" type="data" label="Convert this query" help="GenBank flat file format consists of an annotation section and a sequence section."/>
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7 </inputs>
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8 <outputs>
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9 <data format="gff3" name="gff_format" label="${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_gbk" value="s_cerevisiae_SCU49845.gbk" />
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14 <output name="gff_format" file="s_cerevisiae_SCU49845.gff3" />
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15 </test>
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16 </tests>
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17 <help>
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18
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19 **What it does**
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20
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21 This tool converts data from a GenBank_ flat file format to GFF (scroll down for format description).
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22
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23 .. _GenBank: http://www.ncbi.nlm.nih.gov/genbank/
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24
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25 ------
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26
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27 **Example**
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28
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29 - The following data in GenBank format::
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30
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31 LOCUS NM_001202705 2406 bp mRNA linear PLN 28-MAY-2011
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32 DEFINITION Arabidopsis thaliana thiamine biosynthesis protein ThiC (THIC)
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33 mRNA, complete cds.
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34 ACCESSION NM_001202705
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35 VERSION NM_001202705.1 GI:334184566.........
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36 FEATURES Location/Qualifiers
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37 source 1..2406
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38 /organism="Arabidopsis thaliana"
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39 /mol_type="mRNA"
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40 /db_xref="taxon:3702"........
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41 gene 1..2406
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42 /gene="THIC"
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43 /locus_tag="AT2G29630"
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44 /gene_synonym="PY; PYRIMIDINE REQUIRING; T27A16.27;........
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45 ORIGIN
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46 1 aagcctttcg ctttaggctg cattgggccg tgacaatatt cagacgattc aggaggttcg
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47 61 ttcctttttt aaaggaccct aatcactctg agtaccactg actcactcag tgtgcgcgat
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48 121 tcatttcaaa aacgagccag cctcttcttc cttcgtctac tagatcagat ccaaagcttc
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49 181 ctcttccagc tatggctgct tcagtacact gtaccttgat gtccgtcgta tgcaacaaca
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50 //
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51
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52
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53 - Will be converted to GFF3::
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54
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55 ##gff-version 3
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56 NM_001202705 gbk_to_gff chromosome 1 2406 . + 1 ID=NM_001202705;Alias=2;Dbxref=taxon:3702;Name=NM_001202705
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57 NM_001202705 gbk_to_gff gene 1 2406 . + 1 ID=AT2G29630;Dbxref=GeneID:817513,TAIR:AT2G29630;Name=THIC
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58 NM_001202705 gbk_to_gff mRNA 192 2126 . + 1 ID=AT2G29630.t01;Parent=AT2G29630
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59 NM_001202705 gbk_to_gff CDS 192 2126 . + 1 ID=AT2G29630.p01;Parent=AT2G29630.t01
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60 NM_001202705 gbk_to_gff exon 192 2126 . + 1 Parent=AT2G29630.t01
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61
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62 ------
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63
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64 **About formats**
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65
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66 **GenBank format** An example of a GenBank record may be viewed here_
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67
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68 .. _here: http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
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69
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70 **GFF3** Generic 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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71
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72 1. seqid - Must be a chromosome or scaffold or contig.
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73 2. source - The program that generated this feature.
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74 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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75 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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76 5. stop - The ending position of the feature (inclusive).
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77 6. score - A score between 0 and 1000. If there is no score value, enter ".".
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78 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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79 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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80 9. attributes - All lines with the same group are linked together into a single item.
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81
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82 --------
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83
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84 **Copyright**
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85
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86 2009-2014 Max Planck Society, University of Tübingen & Memorial Sloan Kettering Cancer Center
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87
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88 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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89
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90 </help>
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91 </tool>
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