<tool id="zerone_damid" name="Discretize DamID experiments with Zerone" version="1.0">
    <requirements>
        <requirement type="package" version="1.0">r-zerone</requirement>
        <requirement type="package" version="2.9.3">rpy2</requirement>
        <requirement type="package" version="0.23">pandas</requirement>
        <requirement type="package" version="6.7">click</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/r-zerone.py'
#for c in $control_files:
--control_files '$c'
#end for
#for d in $fusion_files:
--fusion_files '$d'
#end for
--output '$output'
    ]]></command>
    <inputs>
        <param argument="--control_files" type="data" format="bed" multiple="true" label="BED file(s) containing GATC counts for DamID control" help="You can produce these files uing bedtools coverageBed"/>
        <param argument="--fusion_files" type="data" format="bed" multiple="true" label="BED file(s) containing GATC counts for DamID fusion" help="You can produce these files uing bedtools coverageBed"/>
    </inputs>
    <outputs>
        <data name="output" label="Discretized DamID profile for ${on_string}" format="bed"/>
    </outputs>
    <tests>
        <test>
            <param name="control_files" value="c1.bed,c2.bed" ftype="bed"/>
            <param name="damid_files" value="d1.bed,d2.bed" ftype="bed"/>
            <output name="output" value="discrete.bed" ftype="bed"/>
        </test>
    </tests>
    <help><![CDATA[

Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. After the job is done, Zerone checks the results and tells you whether it passes the quality control.

This wrapper uses the zerone R package to discretize quantified GATC counts.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btw336</citation>
    </citations>
</tool>