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1 <tool id="fml_gtf2gff" name="GTF-to-GFF" version="2.0.0">
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2 <description>converter</description>
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3 <command interpreter="python">gtf_to_gff.py $inf_gtf > $gff3_format
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4 </command>
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5 <inputs>
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6 <param format="gtf" name="inf_gtf" type="data" label="Convert this query" help="Provide genome annotation file in GTF."/>
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7 </inputs>
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8 <outputs>
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9 <data format="gff3" name="gff3_format" label="${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_gtf" value="UCSC_transcripts.gtf" />
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14 <output name="gff3_format" file="UCSC_transcripts.gff3" />
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15 </test>
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16 <test>
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17 <param name="inf_gtf" value="JGI_genes.gtf" />
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18 <output name="gff3_format" file="JGI_genes.gff3" />
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19 </test>
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20 <test>
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21 <param name="inf_gtf" value="ENSEMBL_mm9.gtf" />
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22 <output name="gff3_format" file="ENSEMBL_mm9.gff3" />
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23 </test>
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24 <test>
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25 <param name="inf_gtf" value="AceView_ncbi_37.gtf" />
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26 <output name="gff3_format" file="AceView_ncbi_37.gff3" />
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27 </test>
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28 </tests>
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29 <help>
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30
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31 **What it does**
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32
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33 This tool converts data from GTF to a valid GFF3 file (scroll down for format description).
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34
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35 --------
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36
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37 **Example**
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38
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39 - The following data in GTF format::
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40
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41 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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42 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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43 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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44 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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45
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46 - Will be converted to GFF3 format::
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47
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48 ##gff-version 3
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49 17 protein_coding gene 7255208 7258258 . + . ID=ENSG00000213859;Name=KCTD11
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50 17 protein_coding mRNA 7255208 7258258 . + . ID=ENST00000333751;Name=KCTD11-001;Parent=ENSG00000213859
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51 17 protein_coding protein 7256262 7256960 . + . ID=ENSP00000328352;Name=KCTD11-001;Parent=ENST00000333751
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52 17 protein_coding five_prime_UTR 7255208 7256261 . + . Parent=ENST00000333751
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53 17 protein_coding CDS 7256262 7256960 . + 0 Name=CDS:KCTD11;Parent=ENST00000333751,ENSP00000328352
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54 17 protein_coding three_prime_UTR 7256961 7258258 . + . Parent=ENST00000333751
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55 17 protein_coding exon 7255208 7258258 . + . Parent=ENST00000333751
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56
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57 --------
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58
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59 **About formats**
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60
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61 **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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62
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63 1. seqname - The name of the sequence.
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64 2. source - This indicating where the annotation came from.
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65 3. feature - The name of the feature types. The following feature types are required: 'CDS', 'start_codon' and 'stop_codon'
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66 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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67 5. end - The ending position of the feature (inclusive).
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68 6. score - The score field indicates a degree of confidence in the feature's existence and coordinates.
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69 7. strand - Valid entries include '+', '-', or '.'
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70 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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71 9. attributes - These attributes are designed for handling multiple transcripts from the same genomic region.
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72
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73 **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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74
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75 1. seqid - Must be a chromosome or scaffold.
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76 2. source - The program that generated this feature.
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77 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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78 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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79 5. stop - The ending position of the feature (inclusive).
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80 6. score - A score between 0 and 1000. If there is no score value, enter ".".
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81 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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82 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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83 9. attributes - All lines with the same group are linked together into a single item.
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84
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85 --------
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86
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87 **Copyright**
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88
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89 2009-2014 Max Planck Society, University of Tübingen & Memorial Sloan Kettering Cancer Center
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90
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91 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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92
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93 </help>
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94 </tool>
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