<tool id="commonality_r" name="commonality_finder" version="1.0.0">
    <description>finds commonality</description>
    <requirements>
       <requirement type="package">R</requirement>
    </requirements>
    <command><![CDATA[
		ln -s '$input1' input1.csv &&
		ln -s '$input2' input2.csv &&
		ln -s '$input3' input3.csv &&
		ln -s '$input4' input4.csv &&
		ln -s '$input5' input5.csv &&
		ln -s '$input6' input6.csv &&
		
		Rscript '$__tool_directory__/CandD.R' NO NO YES
    ]]></command>
    <inputs>
		<param format="csv" name="input1" type="data" label="First Substrate Set"/>
        <param format="csv" name="input2" type="data" label="First Substrate Background Frequency"/>
		<param format="csv" name="input3" type="data" label="Second Substrate Set"/>
		<param format="csv" name="input4" type="data" label="Second Substrate Background Frequency"/>
		<param format="csv" name="input5" type="data" label="Third Substrate Set"/>
		<param format="csv" name="input6" type="data" label="Third Substrate Background Frequency"/>
		<param name="outGroup" type="text" value="kinase" label="Kinase Name"/>
    </inputs>      
    <outputs>
        <data format="csv" name="substrates" from_work_dir="sharedmotifs.csv" label="${outGroup}_shared Substrates.csv"/>
		<data format="csv" name="SBF" from_work_dir="sharedSBF.csv" label="${outGroup}_shared SBF.csv"/>
    </outputs>
    <tests>
        <test>
            <param name="input1.csv" ftype="csv" value="input1.csv"/>
            <param name="positives" ftype="csv" value="substrates.csv"/>
            <param name="SBF" ftype="csv" value="SBF.csv"/>
			<output name="Negatives" file="negatives.csv"/>
        </test>
    </tests>
    <help><![CDATA[
	This tool uses the output from 3 Kinamine runs to determine what motifs are shared between the three runs
    ]]></help>
    <citations>
        <citation type="doi">10.1021/ja507164a</citation>
    </citations>
</tool>