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1 <tool id="create_annotation_sqlite" name="create annotation in sqlite for trips-viz" version="0.1.4">
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2 <requirements>
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3 <container type="docker">triasteran/trips_create_annotation:latest</container>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 create_annotation_sqlite $annotation $fasta $pseudo_utr_len $transcript $gene $output
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7 ]]></command>
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8 <inputs>
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9 <param format="gtf,gff" name="annotation" type="data" label="GTF/GFF3 File"/>
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10 <param format="fasta" name="fasta" type="data" label="Transcriptome FASTA file"/>
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11 <param name="pseudo_utr_len" type="text" label="Pseudo UTR length"/>
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12 <param name="transcript" type="text" label="Example transcript"/>
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13 <param name="gene" type="text" label="Example gene"/>
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14 </inputs>
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15 <outputs>
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16 <data format="sqlite" name="output" />
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="fasta" value="sacCer3_transcripts.fasta"/>
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21 <param name="annotation" value="saccharomyces_cerevisiae.R64-1-1.84.gtf"/>
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22 <param name="pseudo_utr_len" value="300"/>
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23 <param name="transcript" value="YDL248W"/>
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24 <param name="gene" value="COS7"/>
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25 <output name="output" file="output"/>
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26 </test>
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27 </tests>
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28 <help><![CDATA[
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29 **GTF/GFF3 File**
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30
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31 GFF lines have nine required fields that must be tab-separated.
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32 The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats.
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33
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34 Both transcript ids and gene names should be listed in the file.
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35
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36 -----
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37
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38 **Transcriptome FASTA file**
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39
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40 A FASTA file with an entry for every transcript. The headers should be the transcript id's as they appear in the GTF/GFF3 file.
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41
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42 -----
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43
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44 **Psuedo UTR length**
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45 An integer representing the length (in nucleotides) to be added to the 5' end and 3' end of every transcript with an annotated
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46 CDS. Useful for when an organism does not have any annotated UTR's, if it does use 0. If not 0, the extra nucleotides should
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47 already be present in the FASTA file.
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48
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49 -----
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50
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51 **Example transcript**
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52
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53 An example of a transcript id that appears in the FASTA/GTF/GFF3 file, e.g ENST00000123456
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54
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55 -----
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56
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57 **Example Gene**
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58
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59 An example of a gene name as it appears in the GTF/GFF3 file, e.g BRCA1
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60
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61 -----
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62
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63 **Output**
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64
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65 The output of the script can be downloaded and uploaded to Trips-viz_. by signing in and going to the uploads page, then selecting
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66 "Upload new transcriptome". When uploaded the new organism will appear on the home page of Trips-viz, or under the transcriptomes
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67 page if the organism name used is already present on Trips-viz.
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68
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69
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70
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71 .. _Trips-viz: http://trips.ucc.ie
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72
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73 ]]></help>
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74 <citations>
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75 <citation type="bibtex">
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76 @misc{githubTrips-Viz,
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77 author = {LastTODO, FirstTODO},
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78 year = {TODO},
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79 title = {Trips-Viz},
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80 publisher = {GitHub},
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81 journal = {GitHub repository},
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82 url = {https://github.com/skiniry/Trips-Viz},
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83 }</citation>
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84 </citations>
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85 </tool>
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