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version 1.0
task GffCompare {
input {
File? inputGtfList
Array[File]+? inputGtfFiles
File referenceAnnotation
File? genomeSequences
Int? maxDistanceFreeEndsTerminalExons
Int? maxDistanceGroupingTranscriptStartSites
String? namePrefix
Boolean C = false
Boolean A = false
Boolean X = false
Boolean K = false
Boolean snCorrection = false
Boolean precisionCorrection = false
Boolean discardSingleExonTransfragsAndReferenceTranscripts = false
Boolean discardSingleExonReferenceTranscripts = false
Boolean noTmap = false
Boolean verbose = false
Boolean debugMode = false
}
parameter_meta {}
command {
gffcompare \
-r ~{referenceAnnotation} \
~{"-s " + genomeSequences} \
~{"-e " + maxDistanceFreeEndsTerminalExons} \
~{"-d " + maxDistanceGroupingTranscriptStartSites} \
~{"-p " + namePrefix} \
~{true="-C" false="" C} \
~{true="-A" false="" A} \
~{true="-X" false="" X} \
~{true="-K" false="" K} \
~{true="-R" false="" snCorrection} \
~{true="-Q" false="" precisionCorrection} \
~{true="-M" false="" discardSingleExonTransfragsAndReferenceTranscripts} \
~{true="-N" false="" discardSingleExonReferenceTranscripts} \
~{true="-T" false="" noTmap} \
~{true="-V" false="" verbose} \
~{true="D" false="" debugMode} \
~{"-i " + inputGtfList} \
~{sep=" " + inputGtfFiles}
}
output {}
}