|
0
|
1 <tool id="create_annotation_sqlite" name="Trips-viz:" version="0.1.0">
|
|
|
2 <description>create new organism</description>
|
|
|
3 <command interpreter="python">create_annotation_sqlite.py $annotation $fasta $pseudo_utr_len $transcript $gene $output</command>
|
|
|
4 <inputs>
|
|
|
5 <param format="gtf,gff" name="annotation" type="data" label="GTF/GFF3 File"/>
|
|
|
6 <param format="fasta" name="fasta" type="data" label="Transcriptome FASTA file"/>
|
|
|
7 <param name="pseudo_utr_len" type="text" label="Pseudo UTR length"/>
|
|
|
8 <param name="transcript" type="text" label="Example transcript"/>
|
|
|
9 <param name="gene" type="text" label="Example gene"/>
|
|
|
10 </inputs>
|
|
|
11
|
|
|
12 <outputs>
|
|
|
13 <data format="sqlite" name="output" />
|
|
|
14 </outputs>
|
|
|
15
|
|
|
16 <tests>
|
|
|
17 <test>
|
|
|
18 <param name="input" value="fa_gc_content_input.fa"/>
|
|
|
19 <output name="output" file="saccharomyces_cerevisiae.sqlite"/>
|
|
|
20 </test>
|
|
|
21 </tests>
|
|
|
22
|
|
|
23 <help>
|
|
|
24
|
|
|
25 **GTF/GFF3 File**
|
|
|
26
|
|
|
27 GFF lines have nine required fields that must be tab-separated.
|
|
|
28 The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats.
|
|
|
29
|
|
|
30 Both transcript ids and gene names should be listed in the file.
|
|
|
31
|
|
|
32 -----
|
|
|
33
|
|
|
34 **Transcriptome FASTA file**
|
|
|
35
|
|
|
36 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.
|
|
|
37
|
|
|
38 -----
|
|
|
39
|
|
|
40 **Psuedo UTR length**
|
|
|
41 An integer representing the length (in nucleotides) to be added to the 5' end and 3' end of every transcript with an annotated
|
|
|
42 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
|
|
|
43 already be present in the FASTA file.
|
|
|
44
|
|
|
45 -----
|
|
|
46
|
|
|
47 **Example transcript**
|
|
|
48
|
|
|
49 An example of a transcript id that appears in the FASTA/GTF/GFF3 file, e.g ENST00000123456
|
|
|
50
|
|
|
51 -----
|
|
|
52
|
|
|
53 **Example Gene**
|
|
|
54
|
|
|
55 An example of a gene name as it appears in the GTF/GFF3 file, e.g BRCA1
|
|
|
56
|
|
|
57 -----
|
|
|
58
|
|
|
59 **Output**
|
|
|
60
|
|
|
61 The output of the script can be downloaded and uploaded to Trips-viz_. by signing in and going to the uploads page, then selecting
|
|
|
62 "Upload new transcriptome". When uploaded the new organism will appear on the home page of Trips-viz, or under the transcriptomes
|
|
|
63 page if the organism name used is already present on Trips-viz.
|
|
|
64
|
|
|
65
|
|
|
66
|
|
|
67 .. _Trips-viz: http://trips.ucc.ie
|
|
|
68
|
|
|
69
|
|
|
70 </help>
|
|
|
71 </tool>
|
