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comparison trips_create_annotation/trips_create_annotation.xml @ 0:f24aed7a5cc7 draft

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author jackcurragh
date Mon, 04 Apr 2022 09:30:51 +0000
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1 <tool id="trips_create_annotation" name="Create TRIPS-Viz annotation" version="1.0">
2 <description>Covert GFF3/GTF and transcriptome FASTA to custom annotation sqlite</description>
3 <requirements>
4 <requirement type="package" version="0.19.0">pysam</requirement>
5 <requirement type="package" version="2.0.0">sqlitedict</requirement>
6 <requirement type="package" version="3.37.1">sqlite</requirement>
7 <requirement type="package" version="3.0.2">intervaltree</requirement>
8
9 </requirements>
10 <command><![CDATA[
11 python $__tool_directory__/create_annotation_sqlite.py ${input1} ${input2} ${input3} ${input4} ${input5} ${input6}
12 ]]></command>
13 <inputs>
14 <param name="input1" type="text" label="Transcriptome name" />
15 <param name="input2" type="data" format="gff" label="Transcriptome Annotation file (GFF/GTF)" />
16 <param name="input3" type="data" format="fasta" label="Transcriptome FASTA File" />
17 <param name="input4" type="integer" value="0" label="Psuedo UTR length" help="This value will be added used to create UTRs of this length. This is useful when looking at transcriptomes without annotated UTRs"/>
18 <param name="input5" type="text" label="Transcript ID" help="An example of a transcript_id from the annotation file, e.g ENST000000123456.1"/>
19 <param name="input6" type="text" label="Gene Name" help="An example of a gene name from the annotation file" />
20 </inputs>
21 <outputs>
22 <data name="output1" format="sqlite"/>
23 </outputs>
24 <tests>
25 <test>
26 <param name="input1" value="test_organism" ftype="text"/>
27 <param name="input2" value="test.gtf" ftype="gff"/>
28 <param name="input3" value="test.fasta" ftype="fasta"/>
29 <param name="input4" value="0" ftype="integer"/>
30 <param name="input5" value="YAL012W" ftype="text"/>
31 <param name="input6" value="YDL248W" ftype="text"/>
32 <output name="output1" file="test_organism.sqlite" ftype="sqlite" lines_diff="4" />
33 </test>
34 </tests>
35 <help>
36 **What it does**
37
38 Builds a custom transcirptome annoatation stored in sqlite format for you organism.
39 </help>
40 <citations/>
41 </tool>
42