<tool id="edu.tamu.cpt.util.wigToBigWig" name="Wig to BigWig" version="19.1.0.0" profile="16.04">
    <description>CPT version accepts fasta input for genome lengths.</description>
    <macros>
        <import>macros.xml</import>
    
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="377">ucsc-wigtobigwig</requirement>
    </expand>
    <command detect_errors="aggressive"><![CDATA[
python '$__tool_directory__/fasta_len.py' '$genomes' > 'chrom.len';

grep -v "^track" '$wigFile' |
wigToBigWig -clip stdin chrom.len '$bigwig'
]]></command>
    <inputs>
        <param name="wigFile" type="data" format="wig" label="Wig File"/>
        <param name="genomes" type="data" format="fasta" label="Fasta File" help="File containing fasta sequences referenced by wig file"/>
    </inputs>
    <outputs>
        <data format="bigwig" name="bigwig"/>
    </outputs>
    <tests>
        <test>
            <param name="wigFile" value="T7_BW_I_REBASE.wig"/>
            <param name="genomes" value="T7_CLEAN.fasta"/>
            <output name="bigwig" value="T7_BW_I_REBASE.bigwig"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Convert wig to bigWig
]]></help>
    <expand macro="citations">
        <citation type="doi">10.1093/bioinformatics/btq351</citation>
    </expand>
</tool>