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1 <tool id="fml_gfffmap" name="GFF-map" version="2.0.0">
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2 <description>features</description>
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3 <command interpreter="python">
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4 gff_fmap.py $gff_input > $idmapping
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5 </command>
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6 <inputs>
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7 <param format="gff3,gff" name="gff_input" type="data" label="Query file" help="Provide genome annotation file in GFF."/>
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8 </inputs>
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9 <outputs>
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10 <data format="txt" name="idmapping" label="${tool.name} on ${on_string}: parent child id map"/>
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11 </outputs>
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12 <tests>
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13 <test>
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14 <param name="gff_input" value="Feature_ID_mapping_W.gff3" />
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15 <output name="idmapping" file="Feature_ID_mapping_W.txt" />
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16 </test>
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17 <test>
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18 <param name="gff_input" value="Aly_JGI.gff3" />
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19 <output name="idmapping" file="Feature_ID_mapping_R.txt" />
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20 </test>
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21 </tests>
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22 <help>
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23
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24 **What it does**
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25
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26 GFF-map provides the features (gene, mRNA, UTR's, exon, CDS etc) relationship based on their identifier mapping in a given GFF file.
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27
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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 features ID mapping in the following data in GFF3::
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33
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34 ##gff-version 3
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35 17 protein_coding gene 7255208 7258258 . + . ID=ENSG00000213859;Name=KCTD11
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36 17 protein_coding mRNA 7255208 7258258 . + . ID=ENST00000333751;Name=KCTD11-001;Parent=ENSG00000213859
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37 17 protein_coding protein 7256262 7256960 . + 0 ID=ENSP00000328352;Name=ENSP00000328352
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38 17 protein_coding five_prime_UTR 7255208 7256261 . + . Parent=ENST00000333751
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39 17 protein_coding CDS 7256262 7256960 . + 0 Name=CDS:KCTD11;Parent=ENST00000333751,ENSP00000328352
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40 17 protein_coding three_prime_UTR 7256961 7258258 . + . Parent=ENST00000333751
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41 17 protein_coding exon 7255208 7258258 . + . Parent=ENST00000333751
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42
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43 - Will be displayed as::
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44
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45 +-----------------------+---------------------------------+
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46 | Parent feature type | Associated child feature type(s)|
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47 +-----------------------+---------------------------------+
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48 | protein_coding gene | protein_coding mRNA |
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49 +-----------------------+---------------------------------+
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50 | protein_coding protein| protein_coding CDS |
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51 +-----------------------+---------------------------------+
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52 | protein_coding mRNA | protein_coding CDS |
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53 | | protein_coding exon |
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54 | | protein_coding five_prime_UTR |
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55 | | protein_coding three_prime_UTR |
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56 +-----------------------+---------------------------------+
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57
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58 --------
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59
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60 **About formats**
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61
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62 **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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63
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64 1. seqid - Must be a chromosome or scaffold.
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65 2. source - The program that generated this feature.
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66 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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67 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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68 5. stop - The ending position of the feature (inclusive).
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69 6. score - A score between 0 and 1000. If there is no score value, enter ".".
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70 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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71 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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72 9. attributes - All lines with the same group are linked together into a single item.
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73
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74 --------
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75
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76 **Copyright**
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77
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78 2009-2014 Max Planck Society, University of Tübingen & Memorial Sloan Kettering Cancer Center
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79
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80 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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81
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82 </help>
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83 </tool>
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