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annotate gff_to_gtf.xml @ 10:c42c69aa81f8

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fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo
author vipints <vipin@cbio.mskcc.org>
date Thu, 23 Apr 2015 18:01:45 -0400
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1 <tool id="fml_gff2gtf" name="GFF-to-GTF" version="2.1.0">
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2 <description>converter</description>
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3 <command interpreter="python">gff_to_gtf.py $inf_gff3 &gt; $gtf_format
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4 </command>
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5 <inputs>
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6 <param format="gff3,gff" name="inf_gff3" type="data" label="Convert this query" help="Provide genome annotation file in GFF or GFF3."/>
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7 </inputs>
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8 <outputs>
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9 <data format="gtf" name="gtf_format" label="${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_gff3" value="ens_mm9_chr18.gff3" />
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14 <output name="gtf_format" file="ens_mm9_chr18.gtf" />
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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 GFF to GTF file format (scroll down for format description).
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22
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23 --------
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24
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25 **Example**
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26
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27 - The following data in GFF3::
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28
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29 ##gff-version 3
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30 17 protein_coding gene 7255208 7258258 . + . ID=ENSG00000213859;Name=KCTD11
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31 17 protein_coding mRNA 7255208 7258258 . + . ID=ENST00000333751;Name=KCTD11-001;Parent=ENSG00000213859
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32 17 protein_coding protein 7256262 7256960 . + . ID=ENSP00000328352;Name=KCTD11-001;Parent=ENST00000333751
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33 17 protein_coding five_prime_UTR 7255208 7256261 . + . Parent=ENST00000333751
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34 17 protein_coding CDS 7256262 7256960 . + 0 Name=CDS:KCTD11;Parent=ENST00000333751,ENSP00000328352
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35 17 protein_coding three_prime_UTR 7256961 7258258 . + . Parent=ENST00000333751
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36 17 protein_coding exon 7255208 7258258 . + . Parent=ENST00000333751
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37
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38 - Will be converted to GTF::
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39
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40 17 protein_coding exon 7255208 7258258 . + . gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001";
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41 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";
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42 17 protein_coding start_codon 7256262 7256264 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001";
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43 17 protein_coding stop_codon 7256958 7256960 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001";
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44
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45 --------
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46
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47 **Reference**
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48
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49 **GFF-to-GTF** is part of oqtans package and cited as [1]_.
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50
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51 .. [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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52
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53 .. _10.1093/bioinformatics/btt731: http://goo.gl/I75poH
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54
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55 --------
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56
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57 **About formats**
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58
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59 **GFF format** General 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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60
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61 1. seqid - Must be a chromosome or scaffold.
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62 2. source - The program that generated this feature.
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63 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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64 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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65 5. stop - The ending position of the feature (inclusive).
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66 6. score - A score between 0 and 1000. If there is no score value, enter ".".
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67 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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68 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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69 9. attributes - All lines with the same group are linked together into a single item.
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70
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71 **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::
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72
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73 1. seqname - The name of the sequence.
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74 2. source - This indicating where the annotation came from.
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75 3. feature - The name of the feature types. The following feature types are required: 'CDS', 'start_codon' and 'stop_codon'
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76 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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77 5. end - The ending position of the feature (inclusive).
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78 6. score - The score field indicates a degree of confidence in the feature's existence and coordinates.
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79 7. strand - Valid entries include '+', '-', or '.'
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80 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.
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81 9. attributes - These attributes are designed for handling multiple transcripts from the same genomic region.
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82
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83 --------
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84
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85 **Copyright**
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86
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87 GFF-to-GTF Wrapper Version 0.6 (Apr 2015)
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88
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89 2009-2015 Max Planck Society, University of Tübingen &amp; Memorial Sloan Kettering Cancer Center
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90
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91 </help>
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92 </tool>