<tool id="soft_threshold" name="wgcna soft threshold" version="1.0.0">
    <description>
        Calculate R power table and explore optimal beta value
    </description>
    <stdio>
        <regex match="Execution halted"
               source="both"
               level="fatal"
               description="Execution halted." />
        <regex match="Error in"
               source="both"
               level="fatal"
               description="An undefined error occured, please check your intput carefully and contact your administrator." />
        <regex match="Fatal error"
               source="both"
               level="fatal"
               description="An undefined error occured, please check your intput carefully and contact your administrator." />
    </stdio>
    <requirements>
        <requirement type="package" version="3.2.1">R</requirement>
        <requirement type="package" version="1.0.0">wgcna</requirement>
    </requirements>
    <command>
        <![CDATA[
            Rscript '${__tool_directory__}/soft_threshold.R'
                -t $threads
                -f $expressionData
                -b $betaMaximum
                -r $rPowerTable
                -p $scaleFreeFitPlot
        ]]>
    </command>
    <inputs>
        <param name="threads" type="integer" value="1" label="number of threads for WGCNA"/>
        <param name="expressionData" type="data" format="csv" label="expression data in csv file format. Rows are samples and columns are genes"/>
        <param name="betaMaximum" type="integer" value="12" label="maximum beta values"/>
    </inputs>
    <outputs>
        <data format="csv" name="rPowerTable" label="R power table on ${on_string}" />
        <data format="pdf" name="scaleFreeFitPlot" label="scale free fit plot on ${on_string}" />
    </outputs>
</tool>