<tool id="macs2_bdgcmp" name="MACS2 bdgcmp" version="@VERSION_STRING@.0">
    <description>Deduct noise by comparing two signal tracks in bedGraph</description>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        @home_dir@
        macs2 bdgcmp
            -t '${ infile_treatment }'
            -c '${ infile_control }'

            -m '${ bdgcmp_options.bdgcmp_options_selector }'
            #if str($bdgcmp_options.bdgcmp_options_selector) in ['FE', 'logFE', 'logLR']:
                -p '${ bdgcmp_options.pseudocount }'
            #end if
            -o '${ outfile }'
    ]]></command>
    <inputs>
        <param name="infile_treatment" type="data" format="bedgraph" label="Treatment bedGraph file" />
        <param name="infile_control" type="data" format="bedgraph" label="Control bedGraph file" />

        <conditional name="bdgcmp_options">
            <param name="bdgcmp_options_selector" type="select" label="Method to use while calculating a score in any bin by comparing treatment value and control value" help="Available choices are: ppois, qpois, subtract, logFE, logLR, and slogLR. They represent Poisson Pvalue (-log10(pvalue) form) using control as lambda and treatment as observation, q-value through a BH process for poisson pvalues, subtraction from treatment, linear scale fold enrichment, log10 fold enrichment(need to set pseudocount), log10 likelihood between ChIP-enriched model and open chromatin model(need to set pseudocount), symmetric log10 likelihood between two ChIP-enrichment models, or maximum value between the two tracks. Default=ppois (--method).">
                <option value="ppois" selected="true">Poisson pvalue (-log10) using control as lambda and treatment as observation (ppois)</option>
                <option value="qpois">q-value through a BH process for poisson pvalues (qpois)</option>
                <option value="subtract">subtraction from treatment (subtract)</option>
                <option value="logFE">log10 fold enrichment (logFE)</option>
                <option value="FE">linear scale fold enrichment (FE)</option>
                <option value="logLR">log10 likelihood between ChIP-enriched model and open chromatin model (logLR)</option>
                <option value="slogLR">symmetric log10 likelihood between two ChIP-enrichment models (slogLR)</option>
            </param>
            <when value="FE">
                <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. Default=0.0 (no pseudocount is applied)."/>
            </when>
            <when value="logLR">
                <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. Default=0.0 (no pseudocount is applied)."/>
            </when>
            <when value="logFE">
                <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. Default=0.0 (no pseudocount is applied)."/>
            </when>
            <when value="ppois"/>
            <when value="qpois"/>
            <when value="subtract"/>
            <when value="slogLR"/>
        </conditional>
    </inputs>
    <outputs>
        <data name="outfile" format="bedgraph" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="infile_control" value="bdgcmp_input_control.bdg" ftype="bedgraph"/>
            <param name="infile_treatment" value="bdgcmp_input_treatment.bdg" ftype="bedgraph"/>
            <param name="bdgcmp_options_selector" value="ppois"/>
            <output name="outfile" file="bdgcmp_output.bdg"/>
        </test>
    </tests>
    <help>
        <![CDATA[
**What it does**

This is **bdgcmp** utility from the MACS2_ Package. It is designed to deduct noise by comparing two signal tracks in bedGraph.

.. _MACS2: https://github.com/taoliu/MACS

@citation@
]]>
    </help>
    <expand macro="citations" />
</tool>