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="create annotation in sqlite for trips-viz" version="0.1.0" python_template_version="3.5"> | |
2 <requirements> | |
3 <requirement type="package" version="3.0.2">intervaltree</requirement> | |
4 <requirement type="package" version="3.37.0">sqlite</requirement> | |
5 <requirement type="package" version="0.4.6">pysqlite3</requirement> | |
6 <requirement type="package" version="3.1.0">python-intervaltree</requirement> | |
7 </requirements> | |
8 <command detect_errors="exit_code"><![CDATA[ | |
9 python2 '$__tool_directory__/create_annotation_sqlite.py' $annotation $fasta $pseudo_utr_len $transcript $gene $output | |
10 ]]></command> | |
11 <inputs> | |
12 <param format="gtf,gff" name="annotation" type="data" label="GTF/GFF3 File"/> | |
13 <param format="fasta" name="fasta" type="data" label="Transcriptome FASTA file"/> | |
14 <param name="pseudo_utr_len" type="text" label="Pseudo UTR length"/> | |
15 <param name="transcript" type="text" label="Example transcript"/> | |
16 <param name="gene" type="text" label="Example gene"/> | |
17 </inputs> | |
18 <outputs> | |
19 <data format="sqlite" name="output" /> | |
20 </outputs> | |
21 <tests> | |
22 <test> | |
23 <param name="input" value="fa_gc_content_input.fa"/> | |
24 <output name="output" file="saccharomyces_cerevisiae.sqlite"/> | |
25 </test> | |
26 </tests> | |
27 <help><![CDATA[ | |
28 **GTF/GFF3 File** | |
29 | |
30 GFF lines have nine required fields that must be tab-separated. | |
31 The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats. | |
32 | |
33 Both transcript ids and gene names should be listed in the file. | |
34 | |
35 ----- | |
36 | |
37 **Transcriptome FASTA file** | |
38 | |
39 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. | |
40 | |
41 ----- | |
42 | |
43 **Psuedo UTR length** | |
44 An integer representing the length (in nucleotides) to be added to the 5' end and 3' end of every transcript with an annotated | |
45 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 | |
46 already be present in the FASTA file. | |
47 | |
48 ----- | |
49 | |
50 **Example transcript** | |
51 | |
52 An example of a transcript id that appears in the FASTA/GTF/GFF3 file, e.g ENST00000123456 | |
53 | |
54 ----- | |
55 | |
56 **Example Gene** | |
57 | |
58 An example of a gene name as it appears in the GTF/GFF3 file, e.g BRCA1 | |
59 | |
60 ----- | |
61 | |
62 **Output** | |
63 | |
64 The output of the script can be downloaded and uploaded to Trips-viz_. by signing in and going to the uploads page, then selecting | |
65 "Upload new transcriptome". When uploaded the new organism will appear on the home page of Trips-viz, or under the transcriptomes | |
66 page if the organism name used is already present on Trips-viz. | |
67 | |
68 | |
69 | |
70 .. _Trips-viz: http://trips.ucc.ie | |
71 | |
72 ]]></help> | |
73 <citations> | |
74 <citation type="bibtex"> | |
75 @misc{githubTrips-Viz, | |
76 author = {LastTODO, FirstTODO}, | |
77 year = {TODO}, | |
78 title = {Trips-Viz}, | |
79 publisher = {GitHub}, | |
80 journal = {GitHub repository}, | |
81 url = {https://github.com/skiniry/Trips-Viz}, | |
82 }</citation> | |
83 </citations> | |
84 </tool> |