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annotate fml_gff_converter_programs/galaxy/gff3_to_gtf.xml @ 1:c6cf723c2ed4

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Uploaded version 2.0.0 of gfftools to integrate local Galaxy instances.
author vipints
date Tue, 10 Jun 2014 19:57:56 -0400
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1 <tool id="fml_gff3togtf" name="GFF3_to_GTF" version="1.0.0">
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2 <description>converter</description>
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3 <command interpreter="perl">gff3_to_gtf_converter.pl $inf_gff3 $gtf_format
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4 </command>
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5 <inputs>
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6 <param format="gff3" name="inf_gff3" type="data" label="File in GFF3 format" help="GFF3 format file for converting to GTF."/>
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7 </inputs>
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8 <outputs>
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9 <data format="gtf" name="gtf_format" />
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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="AceView_ncbi_37.gff3" />
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14 <output name="gtf_format" file="AceView_gff3_to_gtf.gtf" />
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15 </test>
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16 <test>
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17 <param name="inf_gff3" value="ENSEMBL_mm9.gff3" />
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18 <output name="gtf_format" file="ENSEMBL_mm9_gff3_to_gtf.gtf" />
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19 </test>
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20 </tests>
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21 <help>
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22
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23 **What it does**
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24
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25 This tool converts data from GFF3 format to GTF format.
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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 GFF3 format::
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32
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33 ##gff-version 3
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34 17 protein_coding gene 7255208 7258258 . + . ID=ENSG00000213859;Name=KCTD11
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35 17 protein_coding mRNA 7255208 7258258 . + . ID=ENST00000333751;Name=KCTD11-001;Parent=ENSG00000213859
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36 17 protein_coding protein 7256262 7256960 . + . ID=ENSP00000328352;Name=KCTD11-001;Parent=ENST00000333751
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37 17 protein_coding five_prime_UTR 7255208 7256261 . + . Parent=ENST00000333751
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38 17 protein_coding CDS 7256262 7256960 . + 0 Name=CDS:KCTD11;Parent=ENST00000333751,ENSP00000328352
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39 17 protein_coding three_prime_UTR 7256961 7258258 . + . Parent=ENST00000333751
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40 17 protein_coding exon 7255208 7258258 . + . Parent=ENST00000333751
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41
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42 - Will be converted to GTF format::
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43
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44 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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45 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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46 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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47 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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48
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49 --------
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50
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51 **About formats**
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52
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53
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54 **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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55
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56 1. seqid - Must be a chromosome or scaffold.
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57 2. source - The program that generated this feature.
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58 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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59 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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60 5. stop - The ending position of the feature (inclusive).
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61 6. score - A score between 0 and 1000. If there is no score value, enter ".".
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62 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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63 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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64 9. attributes - All lines with the same group are linked together into a single item.
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65
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66
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67 **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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68
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69 1. seqname - The name of the sequence.
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70 2. source - This indicating where the annotation came from.
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71 3. feature - The name of the feature types. The following feature types are required: 'CDS', 'start_codon' and 'stop_codon'
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72 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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73 5. end - The ending position of the feature (inclusive).
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74 6. score - The score field indicates a degree of confidence in the feature's existence and coordinates.
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75 7. strand - Valid entries include '+', '-', or '.'
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76 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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77 9. attributes - These attributes are designed for handling multiple transcripts from the same genomic region.
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78
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79 --------
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80
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81 This tool is a part of the **MLB Group at Friedrich Miescher Laboratory of the Max Planck Society**. Copyright (C) 2010 Vipin T. Sreedharan (vipin.ts@tuebingen.mpg.de)
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82 </help>
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83 </tool>