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annotate gbk_to_gff.xml @ 11:5c6f33e20fcc default tip

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requirement tag added
author vipints <vipin@cbio.mskcc.org>
date Fri, 24 Apr 2015 18:04:27 -0400
parents c42c69aa81f8
children
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1 <tool id="fml_gbk2gff" name="GBK-to-GFF" version="2.1.0">
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2 <description>converter</description>
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3 <requirements>
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4 <requirement type="package" version="1.65">biopython</requirement>
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5 </requirements>
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6 <command interpreter="python">gbk_to_gff.py $inf_gbk &gt; $gff_format
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7 </command>
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8 <inputs>
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9 <param format="gb,gbk,genbank" name="inf_gbk" type="data" label="Convert this query" help="GenBank flat file format consists of an annotation section and a sequence section."/>
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10 </inputs>
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11 <outputs>
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12 <data format="gff" name="gff_format" label="${tool.name} on ${on_string}: Converted"/>
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13 </outputs>
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14 <tests>
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15 <test>
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16 <param name="inf_gbk" value="s_cerevisiae_SCU49845.gbk" />
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17 <output name="gff_format" file="s_cerevisiae_SCU49845.gff" />
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18 </test>
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19 </tests>
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20 <help>
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21
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22 **What it does**
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23
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24 This tool converts data from a GenBank_ flat file format to GFF (scroll down for format description).
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25
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26 .. _GenBank: http://www.ncbi.nlm.nih.gov/genbank/
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28 ------
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29
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30 **Example**
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31
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32 - The following data in GenBank format::
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33
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34 LOCUS NM_001202705 2406 bp mRNA linear PLN 28-MAY-2011
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35 DEFINITION Arabidopsis thaliana thiamine biosynthesis protein ThiC (THIC)
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36 mRNA, complete cds.
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37 ACCESSION NM_001202705
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38 VERSION NM_001202705.1 GI:334184566.........
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39 FEATURES Location/Qualifiers
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40 source 1..2406
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41 /organism="Arabidopsis thaliana"
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42 /mol_type="mRNA"
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43 /db_xref="taxon:3702"........
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44 gene 1..2406
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45 /gene="THIC"
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46 /locus_tag="AT2G29630"
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47 /gene_synonym="PY; PYRIMIDINE REQUIRING; T27A16.27;........
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48 ORIGIN
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49 1 aagcctttcg ctttaggctg cattgggccg tgacaatatt cagacgattc aggaggttcg
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50 61 ttcctttttt aaaggaccct aatcactctg agtaccactg actcactcag tgtgcgcgat
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51 121 tcatttcaaa aacgagccag cctcttcttc cttcgtctac tagatcagat ccaaagcttc
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52 181 ctcttccagc tatggctgct tcagtacact gtaccttgat gtccgtcgta tgcaacaaca
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53 //
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54
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55
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56 - Will be converted to GFF3::
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57
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58 NM_001202705 gbk2gff chromosome 1 2406 . + 1 ID=NM_001202705;Alias=2;Dbxref=taxon:3702;Name=NM_001202705
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59 NM_001202705 gbk2gff gene 1 2406 . + 1 ID=AT2G29630;Dbxref=GeneID:817513,TAIR:AT2G29630;Name=THIC
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60 NM_001202705 gbk2gff mRNA 192 2126 . + 1 ID=AT2G29630.t01;Parent=AT2G29630
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61 NM_001202705 gbk2gff CDS 192 2126 . + 1 ID=AT2G29630.p01;Parent=AT2G29630.t01
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62 NM_001202705 gbk2gff exon 192 2126 . + 1 Parent=AT2G29630.t01
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63
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64 ------
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65
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66 **Reference**
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67
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68 **GBK-to-GFF** is part of oqtans package and cited as [1]_.
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69
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70 .. [1] Sreedharan VT, Schultheiss SJ, Jean G et.al., Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. Bioinformatics (2014). `10.1093/bioinformatics/btt731`_
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71
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72 .. _10.1093/bioinformatics/btt731: http://goo.gl/I75poH
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73
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74 ------
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75
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76 **About file formats**
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77
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78 **GenBank format** An example of a GenBank record may be viewed here_
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79
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80 .. _here: http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
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81
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82 **GFF** Generic Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF lines have nine tab-separated fields::
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83
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84 1. seqid - Must be a chromosome or scaffold or contig.
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85 2. source - The program that generated this feature.
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86 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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87 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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88 5. stop - The ending position of the feature (inclusive).
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89 6. score - A score between 0 and 1000. If there is no score value, enter ".".
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90 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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91 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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92 9. attributes - All lines with the same group are linked together into a single item.
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93
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94 --------
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95
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96 **Copyright**
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97
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98 GBK-to-GFF Wrapper Version 0.6 (Apr 2015)
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99
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100 2009-2015 Max Planck Society, University of Tübingen &amp; Memorial Sloan Kettering Cancer Center
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101
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102 </help>
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103 </tool>