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<paramargument="--UTR"type="boolean"checked="false"truevalue="--UTR=on"falsevalue=""label=""help="Experimental, requires RNASeq data (bam) and a softmasked genome" />
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<paramargument="--filterOutShort"type="boolean"checked="false"truevalue="--filterOutShort"falsevalue=""label="Filter out too short traingin gene predicted by GeneMark-EX" />
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<paramargument="--filterOutShort"type="boolean"checked="false"truevalue="--filterOutShort"falsevalue=""label="Filter out too short training gene predicted by GeneMark-EX" />
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<paramargument="--eval"type="data"format="gtf"optional="true"label="Reference set to evaluate predictions"help="using evaluation scripts from GaTech" />
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<paramargument="--eval_pseudo"type="data"format="gff3"optional="true"label="File with pseudogenes that will be excluded from accuracy evaluation" />
<!--param argument="-\-UTR" type="boolean" checked="false" truevalue="-\-UTR=on" falsevalue="" label="" help="Experimental, requires RNASeq data (bam) and a softmasked genome" /-->
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<paramargument="--filterOutShort"type="boolean"checked="false"truevalue="--filterOutShort"falsevalue=""label="Filter out too short traingin gene predicted by GeneMark-EX" />
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<paramargument="--filterOutShort"type="boolean"checked="false"truevalue="--filterOutShort"falsevalue=""label="Filter out too short training gene predicted by GeneMark-EX" />
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<paramargument="--eval"type="data"format="gtf"optional="true"label="Reference set to evaluate predictions"help="using evaluation scripts from GaTech" />
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<paramargument="--eval_pseudo"type="data"format="gff3"optional="true"label="File with pseudogenes that will be excluded from accuracy evaluation" />
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<paramargument="--alternatives-from-evidence"type="boolean"checked="true"truevalue="--alternatives-from-evidence=true"falsevalue="--alternatives-from-evidence=false"label="Output alternative transcripts based on explicit evidence from hints"/>
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