<tool id="commonality_r" name="difference_finder" version="1.0.0">
    <description>finds differences</description>
    <requirements>
       <requirement type="package">R</requirement>
    </requirements>
    <command><![CDATA[
		ln -s '$input1' S1.csv &&
		ln -s '$input2' SBF1.csv &&
		ln -s '$input3' S2.csv &&
		ln -s '$input4' SBF2.csv &&
		
		Rscript '$__tool_directory__/Difference finder MADE 7 TO 7 4-18-2019.R'
    ]]></command>
    <inputs>
		<param format="csv" name="input1" type="data" label="First Substrate Set"/>
		<param format="csv" name="input2" type="data" label="First Substrate Background Frequency"/>
		<param format="csv" name="input3" type="data" label="Second Substrate Set"/>
		<param format="csv" name="input4" type="data" label="Second Substrate Background Frequency"/>
		<param name="outGroup" type="text" value="kinase" label="Kinase Name"/>
    </inputs>      
    <outputs>
		<data format="csv" name="substrates1" from_work_dir="1RS.csv" label="${outGroup}_First_Unshared_Substrates.csv"/>
		<data format="csv" name="SBF1" from_work_dir="1RSBF.csv" label="${outGroup}_First_Unshared_SBF.csv"/>
		 <data format="csv" name="substrates2" from_work_dir="2RS.csv" label="${outGroup}_Second_Unshared_Substrates.csv"/>
		<data format="csv" name="SBF2" from_work_dir="2RSBF.csv" label="${outGroup}_Second_Unshared_SubstratesSBF.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 takes two Kinamine outputs (substrates and substrate background frequency files) and finds the symmetrical differences between those sets
	
	Let us call the two INPUT substrate files 'Substrates A' and 'Substrates B'.  Let us call the two OUTPUT substrate files 'Substrates Y' and 'Substrates Z'.  If we treat each file as a SET, then...
	
	'Substrates Y' consists of all 'Substrates A' that are not in 'Substrates B'.  'Substrates Z' consists of all 'Substrates B' that are not in 'Substrates A'.  
	
	The associated Substrate Background Frequency files for each consists of all the proteins associated with that substrate file.
    ]]></help>
    <citations>
        <citation type="doi">10.1074/mcp.RA118.001111</citation>
    </citations>
</tool>