input.xml

<?xml version="1.0" encoding="UTF-8"?>
<inputConfig>
    <workflow>FalseDiscoveryRate,Threshold,Mzid2Csv</workflow>
    <outputFolder>C:\Users\Josh\Desktop\Workspace\bioOutput</outputFolder>
    <uniqueId>testRun1</uniqueId>
    <modules>
        <module>
            <name>FalseDiscoveryRateGlobal</name>
            <input>
                ["Inputfile:C:\Users\Josh\Desktop\Workspace\bioliner-test\55merge_tandem.xml.mzid","outputfile:fdr-result.mzid","-decoyValue 1 -decoyRegex REVERSED -cvTerm MS:1002356 -betterScoresAreLower true -fdrLevel Peptide -proteinLevel PAG -compress false"]
            </input>
        </module>
        <module>
            <name>Threshold</name>
            <input>
                ["Inputfile:fdr-result.mzid","outputfile:thr-result.mzid","-isPSMThreshold true -cvAccessionForScoreThreshold MS:1002125 -threshValue 0.01 -betterScoresAreLower false -deleteUnderThreshold true -compress false"]
            </input>
        </module>
        <module>
            <name>Mzid2Csv</name>
            <input>
                ["Inputfile:thr-result.mzid","outputfile:final-result.csv","-exportType exportPSMs -verboseOutput false -compress false"]
            </input>
        </module>
    </modules>
</inputConfig>