Mercurial > repos > triasteran > trips_create_new_organism

comparison final/create_annotation_sqlite.xml @ 4:9482a43a3d83 draft

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author triasteran
date Tue, 01 Mar 2022 12:40:17 +0000
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3:d55c72b843d9 4:9482a43a3d83
1 <tool id="create_annotation_sqlite" name="create annotation in sqlite for trips-viz" version="0.1.4">
2 <requirements>
3 <container type="docker">triasteran/trips_create_annotation:latest</container>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 create_annotation_sqlite $annotation $fasta $pseudo_utr_len $transcript $gene $output
7 ]]></command>
8 <inputs>
9 <param format="gtf,gff" name="annotation" type="data" label="GTF/GFF3 File"/>
10 <param format="fasta" name="fasta" type="data" label="Transcriptome FASTA file"/>
11 <param name="pseudo_utr_len" type="text" label="Pseudo UTR length"/>
12 <param name="transcript" type="text" label="Example transcript"/>
13 <param name="gene" type="text" label="Example gene"/>
14 </inputs>
15 <outputs>
16 <data format="sqlite" name="output" />
17 </outputs>
18 <tests>
19 <test>
20 <param name="fasta" value="sacCer3_transcripts.fasta"/>
21 <param name="annotation" value="saccharomyces_cerevisiae.R64-1-1.84.gtf"/>
22 <param name="pseudo_utr_len" value="300"/>
23 <param name="transcript" value="YDL248W"/>
24 <param name="gene" value="COS7"/>
25 <output name="output" file="output"/>
26 </test>
27 </tests>
28 <help><![CDATA[
29 **GTF/GFF3 File**
30
31 GFF lines have nine required fields that must be tab-separated.
32 The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats.
33
34 Both transcript ids and gene names should be listed in the file.
35
36 -----
37
38 **Transcriptome FASTA file**
39
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.
41
42 -----
43
44 **Psuedo UTR length**
45 An integer representing the length (in nucleotides) to be added to the 5' end and 3' end of every transcript with an annotated
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
47 already be present in the FASTA file.
48
49 -----
50
51 **Example transcript**
52
53 An example of a transcript id that appears in the FASTA/GTF/GFF3 file, e.g ENST00000123456
54
55 -----
56
57 **Example Gene**
58
59 An example of a gene name as it appears in the GTF/GFF3 file, e.g BRCA1
60
61 -----
62
63 **Output**
64
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
66 "Upload new transcriptome". When uploaded the new organism will appear on the home page of Trips-viz, or under the transcriptomes
67 page if the organism name used is already present on Trips-viz.
68
69
70
71 .. _Trips-viz: http://trips.ucc.ie
72
73 ]]></help>
74 <citations>
75 <citation type="bibtex">
76 @misc{githubTrips-Viz,
77 author = {LastTODO, FirstTODO},
78 year = {TODO},
79 title = {Trips-Viz},
80 publisher = {GitHub},
81 journal = {GitHub repository},
82 url = {https://github.com/skiniry/Trips-Viz},
83 }</citation>
84 </citations>
85 </tool>