Mercurial > repos > jackcurragh > trips_viz_create_annotation

comparison trips_create_annotation/trips_create_annotation.xml @ 3:f1c72ed4b32c draft

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author jackcurragh
date Wed, 20 Apr 2022 15:18:02 +0000
parents d70696d3341e
children 0558d4e0f1cf
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2:d70696d3341e 3:f1c72ed4b32c
5 <requirement type="package" version="2.0.0">sqlitedict</requirement> 5 <requirement type="package" version="2.0.0">sqlitedict</requirement>
6 <requirement type="package" version="3.37.1">sqlite</requirement> 6 <requirement type="package" version="3.37.1">sqlite</requirement>
7 <requirement type="package" version="3.0.2">intervaltree</requirement> 7 <requirement type="package" version="3.0.2">intervaltree</requirement>
8 8
9 </requirements> 9 </requirements>
10 <command><![CDATA[ 10 <command>
11 python $__tool_directory__/create_annotation_sqlite.py ${input1} ${input2} ${input3} ${input4} ${input5} ${input6} 11 python $__tool_directory__/create_annotation_sqlite.py ${output1} ${input2} ${input3} ${input4} ${input5} ${input6} ${output1}
12 ]]></command> 12 </command>
13 <inputs> 13 <inputs>
14 <param name="input1" type="text" label="Transcriptome name" /> 14 <param name="input1" type="text" label="Transcriptome name" help="This will be the outputs filename (No Spaces!)"/>
15 <param name="input2" type="data" format="gff" label="Transcriptome Annotation file (GFF/GTF)" /> 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" /> 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"/> 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"/> 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" /> 19 <param name="input6" type="text" label="Gene Name" help="An example of a gene name from the annotation file" />
33 </test> 33 </test>
34 </tests> 34 </tests>
35 <help> 35 <help>
36 **What it does** 36 **What it does**
37 37
38 Builds a custom transcirptome annoatation stored in sqlite format for you organism. 38 Builds a custom transcirptome annoatation stored in sqlite format for your organism.
39 </help> 39 </help>
40 <citations/> 40 <citations/>
41 </tool> 41 </tool>
42 42