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<tool id="notos" name="Analyse CpGo/e ratios" version="1.0.0">
    <requirements>
        <requirement type="package" version="3.2.1">R</requirement>
        <requirement type="package" version="1.0.0">notos</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
		Rscript ${__tool_directory__}/KDEanalysis.r
		-o $fracOutl
		-d $minDist
		-c $confLevel
		-m $modeMass
		-b $bandWidth
		#if $bootstrap == "TRUE"
		-B
		#end if
		-r $BSrep
		#if $nofew == "TRUE"
			-f
		#end if
		"$species"
		$cpgoe
    ]]></command>
		<inputs>
			<param name="species" size="30" type="text" value="my_species" label="Species name" />
		    <param name="cpgoe" type="data" format="tabular" />
			<param name="fracOutl" type="float" value="0.01" help="maximum fraction of CpGo/e ratios excluded as outliers" label= "max fraction of CpGo/e ratios excluded as outliers" />
			<param name="minDist" type="float" value="0.2" help="minimum distance between modes. Modes that are closer are joined" label= "min distance between modes to join" />
			<param name="confLevel" type="float" value="0.95" help="level of the confidence intervals of the mode positions" label= "level of the confidence intervals of the mode positions" />
			<param name="modeMass" type="float" value="0.05" help="minimum probability mass of a mode " label= "minimum probability mass of a mode" />
			<param name="bandWidth" type="float" value="1.06" help="bandwidth constant for kernels " label= "bandwidth constant for kernels" />
			<param name="bootstrap" type="boolean" truevalue="TRUE" falsevalue="FALSE" help="calculate confidence intervals of mode positions using bootstrap" label= "bootstrap confidence intervals?" />
			<param name="BSrep" type="integer" value="1500" help="number of bootstrap repetitions " label= "number of bootstrap repetitions " />
			<param name="nofew" type="boolean" truevalue="TRUE" falsevalue="FALSE" help="Do not print warning message when few datapoint are given." label= "Supress few datapoint warning" />
		</inputs>
		<outputs>
			<data name="summary" format="tabular" from_work_dir="summary.csv" label="Summary on ${on_string}" />
			<data name="outlierHist" format="pdf" from_work_dir="outliers_hist.pdf" label="Outlier Histogram on ${on_string}"/>
			<data name="cutoff" format="tabular" from_work_dir="outliers_cutoff.csv" label="Outlier cutoff on ${on_string}" />
			<data name="peaks" format="tabular" from_work_dir="modes_basic_stats.csv" label="Peaks on ${on_string}" />
			<data name="kde" format="pdf" from_work_dir="KDE.pdf" label="KDE analysis on ${on_string}" />
		</outputs>
    <tests>
        <test>
            <param name="cpgoe" value="10_std_unif.txt"/>
            <output name="cutoff1" file="outliers_cutoff.csv"/>
			<!--
            <output name="outlierHist" file="outliers_hist.pdf"/>
            <output name="kde" file="KDE.pdf"/>
			-->
        </test>
    </tests>
    <help><![CDATA[
Model the distribution of CpG o/e ratios using Kernel Density Estimation.

Parameters::

  "-o", "--frac-outl"			maximum fraction of CpGo/e ratios excluded as outliers [default 0.01]
  "-d", "--min-dist"			minimum distance between modes, modes that are closer are joined [default 0.2]
  "-c", "--conf-level"			level of the confidence intervals of the mode positions [default 0.95]
  "-m", "--mode-mass"			minimum probability mass of a mode [default 0.05]
  "-b", "--band-width"			bandwidth constant for kernels [default 1.06]
  "-B", "--bootstrap"			calculate confidence intervals of mode positions using bootstrap.
  "-r", "--bootstrap-reps"		number of bootstrap repetitions [default 1500]
  "-p", "--peak-file"			name of the output file describing the peaks of the KDE [default peaks.csv]
  "-s", "--bootstrap-file"		Name of the output file with bootstrap values [default "bootstrap.csv"]
  "-H", "--outlier-hist-file"	Outliers histogram file [default outliers_hist.pdf]
  "-C", "--cutoff-file"			Outliers cutoff file [default outliers_cutoff.csv]
  "-k", "--kde-file"			Kernel density estimation graph [default KDE.pdf]


    ]]></help>
    <citations>
            <citation type="doi">10.1101/180463</citation>
    </citations>
</tool>