<tool id="trips_create_annotation" name="Create TRIPS-Viz annotation" version="1.0">
    <description>Covert GFF3/GTF and transcriptome FASTA to custom annotation sqlite</description>
    <requirements>
        <requirement type="package" version="0.19.0">pysam</requirement>
        <requirement type="package" version="2.0.0">sqlitedict</requirement>
        <requirement type="package" version="3.37.1">sqlite</requirement>
        <requirement type="package" version="3.0.2">intervaltree</requirement>

    </requirements>
    <command>
        python $__tool_directory__/create_annotation_sqlite.py ${output1} ${input2} ${input3} ${input4} ${input5} ${input6} ${output1}
    </command>
    <inputs>
        <param name="input1" type="text" label="Transcriptome name" help="This will be the outputs filename (No Spaces!)"/>
        <param name="input2" type="data" format="gff" label="Transcriptome Annotation file (GFF/GTF)" />
        <param name="input3" type="data" format="fasta" label="Transcriptome FASTA File" />
        <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"/>
        <param name="input5" type="text" label="Transcript ID" help="An example of a transcript_id from the annotation file, e.g ENST000000123456.1"/>
        <param name="input6" type="text" label="Gene Name" help="An example of a gene name from the annotation file" />
    </inputs>
    <outputs>
       <data name="output1" format="sqlite"/>
    </outputs>
    <tests>
        <test>
        <param name="input1" value="test_org" ftype="text"/>
        <param name="input2" value="test.gtf" ftype="gff"/>
        <param name="input3" value="test.fasta" ftype="fasta"/>
        <param name="input4" value="0" ftype="integer"/>
        <param name="input5" value="YDL248W" ftype="text"/>
        <param name="input6" value="YDL248W" ftype="text"/>
        <output name="output1" file="test_org.sqlite" ftype="sqlite" lines_diff="4" />
        </test>
    </tests>
    <help>
    **What it does**

    Builds a custom transcirptome annoatation stored in sqlite format for your organism.
    </help>
    <citations/>
</tool>