Mercurial > repos > triasteran > trips_create_new_organism
comparison trips_create_new_organism/create_annotation_sqlite_.xml @ 0:c5a566609a25 draft
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author | triasteran |
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date | Fri, 25 Feb 2022 11:24:50 +0000 |
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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> |