<tool id="qq_manhattan" name="Manhattan Plots" version="0.1.0" profile="19.05">
    <requirements>
        <requirement type="package" version="0.1.4">r-qqman</requirement>
        <requirement type="package" version="1.6.4">r-optparse</requirement>
    </requirements>
    <command detect_errors='exit_code'><![CDATA[
        Rscript $__tool_directory__/manhattan.R --file '$data' --pval '$pval' --chr '$chr' --bp '$bp' --snp '$snp' --name '$name'
    ]]></command>
    <inputs>
        <param name="data" type="data" format="tabular,tsv" label="Data file"/>
        <param name="pval" type="text" value="P" label="P-value column name in input file"/>
        <param name="chr" type="text" value="CHR" label="Chromosome column name in input file"/>
        <param name="bp" type="text" value="BP" label="Base pair coordinate column name in input file"/>
        <param name="snp" type="text" value="SNP" label="SNP ID column name in input file"/>
        <param name="name" type="text" value="Manhattan Plot" label="Plot title"/>
    </inputs>
    <outputs>
        <data format="pdf" name="manhattan" from_work_dir="manhattan.pdf"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="data" value="test.tsv"/>
            <output name="manhattan" file="manhattan.pdf" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
        Simple manhattan plot wrapper usinng the qqman bioconductor package.
    ]]></help>
    <citations>
        <citation type="doi">https://doi.org/10.1101/005165</citation>
    </citations>
</tool>