<tool id="damidseq_find_peaks" name="damidseq find peaks" version="0.1.3">
    <description>Simple FDR random permutation peak caller</description>
    <requirements>
        <requirement type="package" version="5.26">perl</requirement>
    </requirements>
    <version_command><![CDATA[perl '$__tool_directory__/find_peaks' --help 2>&1| grep find_peaks]]></version_command>
    <command detect_errors="aggressive"><![CDATA[
perl '$__tool_directory__/find_peaks'
 --fdr=$fdr
 --frac=$fdr
 --min_count=$min_count
 --min_quant=$min_quant
 --n=$n
 --step=$step
 --unified_peaks=$unified_peaks
 '$input_file' | LC_ALL=C sed -e 's/[^A-Za-z0-9._-]/ /g' && 
mv peak_analysis*/*.gff peaks.gff &&
mv peak_analysis*/*data log.txt
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="gff,bed,bedgraph" label="Select dam-fusion/dam ratio files" help="You can use damidseq_core to produce this file."/>
        <param argument="--fdr" type="float" min="0" max="1" value="0.01" label="Set the False Discovery Rate (FDR)"/>
        <param argument="--frac" type="float" min="0" max="1" value="0.01" label="Number of random fragments to consider per iteration"/>
        <param argument="--min_count" type="integer" min="1" value="2" label="Minimum number of fragments to consider as a peak"/>
        <param argument="--min_quant" type="float" min="0" max="1" value="0.95" label="Minimum quantile for considering peaks"/>
        <param argument="--n" type="integer" min="1" value="100" label="Number of iterations"/>
        <param argument="--step" type="float" min="0" max="1" value="0.01" label="Stepping for quantiles"/>
        <param argument="--unified_peaks" type="select" label="Set the False Discovery Rate (FDR)">
            <option value="max">call maximum overlap as peak</option>
            <option value="min">call minimum overlap as peak</option>
        </param>
    </inputs>
    <outputs>
        <data name="peaks" format="gff3" from_work_dir="peaks.gff" label="${tool.name} on ${on_string}"/>
        <data name="logs" format="txt" hidden="true" from_work_dir="log.txt" label="${tool.name} logs on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="hp1.bed" ftype="bed"/>
            <param name="min_count" value="1"/>
            <param name="fdr" value="0.1"/>
            <output name="peaks" value="peaks.gff"/>
        </test>
    </tests>
    <help><![CDATA[

Options:
 --fdr            False discovery rate value
                    [Current value: 0.01]
 --frac           Number of random fragments to consider per iteration
 --min_count      Minimum number of fragments to consider as a peak
                    [Current value: 2]
 --min_quant      Minimum quantile for considering peaks
                    [Current value: 0.95]
 --n              Number of iterations
                    [Current value: 100]
 --step           Stepping for quantiles
                    [Current value: 0.01]
 --unified_peaks  Method for calling peak overlaps (two options):
                    'min': call minimum overlapping peak area
                    'max': call maximum overlap as peak
                    [Current value: max]

        ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btv386</citation>
    </citations>
</tool>