<tool id="span" name="SPAN" version="0.7.1.4272">
    <description>ChIP-Seq analysis</description>
    <requirements>
        <requirement type="package" version="0.7.1.4272">package_span_jar</requirement>
        <!--<container type="docker">biolabs/span</container>-->
    </requirements>
    <stdio>
        <!-- Wrapper ensures anything other than zero is an error -->
        <exit_code range="1:"/>
        <exit_code range=":-1"/>
    </stdio>
    <command interpreter="python">
#if str($action.action_selector) == "model"
    #if $control.control_selector
        span_wrapper.py model with_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${control.control_file}"
    #else
        span_wrapper.py model without_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}"
    #end if
#else
    #if $control.control_selector
        span_wrapper.py peaks with_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${control.control_file}" "${fdr}" "${gap}" "${action.peaks_file}"
    #else
        span_wrapper.py peaks without_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${fdr}" "${gap}" "${action.peaks_file}"
    #end if
#end if
     </command>
    <inputs>
        <param name="treatment_file" type="data" format="bam" label="Treatment BAM"
               description="Treatment BAM reads to process"/>
        <param name="genome" type="data" format="chrom.sizes" label="Genome chrom.sizes"
               description="Genome build chrom.sizes file"/>

        <conditional name="control">
            <param name="control_selector" type="boolean" label="Control available" value="false"/>
            <when value="true">
                <param name="control_file" type="data" format="bam" label="Control BAM"
                       description="Control BAM reads to process"/>
            </when>
        </conditional>

        <conditional name="action">
            <param name="action_selector" type="select" label="Action">
                <option value="model">Compute SPAN model</option>
                <option value="peaks">Compute SPAN model and produce peaks file</option>
            </param>
            <when value="model">
                <param name="model_file" type="text" value="model.span" label="Model name"/>
            </when>
            <when value="peaks">
                <param name="model_file" type="text" value="model.span" label="Model file name"/>
                <param name="fdr" size="5" type="float" value="0.0001" label="FDR"/>
                <param name="gap" size="5" type="integer" value="5" label="GAP"/>
                <param name="peaks_file" type="text" value="result.peak" label="Peaks file name"/>
            </when>
        </conditional>

        <param name="bin" size="5" type="integer" value="200" label="Bin size"/>
    </inputs>
    <outputs>
        <data name="${action.model_file}" format="span" label="SPAN model file"/>
        <data name="${action.peaks_file}" format="bed" label="SPAN peaks file">
            <filter>action['action_selector'] == "peaks"</filter>
        </data>
    </outputs>
    <help>
        SPAN Semi-supervised Peak Analyzer is a tool for analyzing ChIP-seq data.
        Details: http://artyomovlab.wustl.edu/aging/span.html
    </help>
</tool>