<tool id="create_gffdb" name="Create gffutils SQLite DB" version="0.1.0">
    <description>for GTF or GFF3</description>
    <requirements>
        <requirement type="package">gffutils</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/create_gffdb.py' $disable_infer_transcripts $disable_infer_genes $create_introns '$input' '$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="gtf,gff3" label="GTF or GFF3 Annotation"/>
        <param name="create_introns" type="boolean" truevalue="--create_introns" falsevalue="" checked="false" 
             label="create intron features"/>
        <param name="disable_infer_transcripts" type="boolean" truevalue="--disable_infer_transcripts" falsevalue="" checked="true" 
             label="disable_infer_transcripts (True for Ensmbl GTF)"
             help="Can be more than 100 times slower if this is false"/>
        <param name="disable_infer_genes" type="boolean" truevalue="--disable_infer_genes" falsevalue="" checked="true" 
             label="disable_infer_transcripts (True for Ensmbl GTF)"
             help="Can be more than 100 times slower if this is false"/>
    </inputs>
    <outputs>
        <data name="output" format="sqlite" label="${tool.name} ${input.name}.sqlite" />
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="gtf" value="GRCm38.gtf"/>
            <output name="output" file="GRCm38.gtf.sqlite" ftype="sqlite" compare="sim_size" delta="5000" />
        </test>
        <test>
            <param name="input" ftype="gff3" value="GRCm38.gff3"/>
            <output name="output" file="GRCm38.gff3.sqlite" ftype="sqlite" compare="sim_size" delta="5000" />
        </test>
    </tests>
    <help><![CDATA[
Creates a SQLite database for a GTF or GFF3 feature file.   
http://daler.github.io/gffutils/index.html
    ]]></help>
</tool>