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1 <tool id="create_annotation_sqlite" name="create annotation in sqlite for trips-viz" version="0.1.1">
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2 <requirements>
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3 <requirement type="package" version="0.4.6">pysqlite3</requirement>
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4 <requirement type="package" version="3.1.0">python-intervaltree</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python2 '$__tool_directory__/create_annotation_sqlite.py' $annotation $fasta $pseudo_utr_len $transcript $gene $output
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8 ]]></command>
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9 <inputs>
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10 <param format="gtf,gff" name="annotation" type="data" label="GTF/GFF3 File"/>
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11 <param format="fasta" name="fasta" type="data" label="Transcriptome FASTA file"/>
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12 <param name="pseudo_utr_len" type="text" label="Pseudo UTR length"/>
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13 <param name="transcript" type="text" label="Example transcript"/>
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14 <param name="gene" type="text" label="Example gene"/>
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15 </inputs>
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16 <outputs>
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17 <data format="sqlite" name="output" />
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="input" value="fa_gc_content_input.fa"/>
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22 <output name="output" file="saccharomyces_cerevisiae.sqlite"/>
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23 </test>
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24 </tests>
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25 <help><![CDATA[
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26 **GTF/GFF3 File**
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27
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28 GFF lines have nine required fields that must be tab-separated.
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29 The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats.
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30
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31 Both transcript ids and gene names should be listed in the file.
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32
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33 -----
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34
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35 **Transcriptome FASTA file**
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36
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37 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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38
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39 -----
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40
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41 **Psuedo UTR length**
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42 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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43 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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44 already be present in the FASTA file.
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45
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46 -----
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47
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48 **Example transcript**
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49
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50 An example of a transcript id that appears in the FASTA/GTF/GFF3 file, e.g ENST00000123456
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51
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52 -----
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53
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54 **Example Gene**
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55
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56 An example of a gene name as it appears in the GTF/GFF3 file, e.g BRCA1
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57
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58 -----
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59
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60 **Output**
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61
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62 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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63 "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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64 page if the organism name used is already present on Trips-viz.
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65
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66
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67
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68 .. _Trips-viz: http://trips.ucc.ie
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69
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70 ]]></help>
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71 <citations>
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72 <citation type="bibtex">
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73 @misc{githubTrips-Viz,
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74 author = {LastTODO, FirstTODO},
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75 year = {TODO},
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76 title = {Trips-Viz},
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77 publisher = {GitHub},
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78 journal = {GitHub repository},
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79 url = {https://github.com/skiniry/Trips-Viz},
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80 }</citation>
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81 </citations>
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82 </tool> |
