comparison braker3.xml @ 8:a9b0b926e133 draft default tip

planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6f7fd50bc001327f69d5391d236aecba0eb64b3

7:c42bf6424ba4

            <param argument="--keepCrf" type="boolean" checked="false" truevalue="--keepCrf" falsevalue="" label="CRF parameters" help="keep CRF parameters even if they are no better than HMM parameters"/>
        </section>

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

8:a9b0b926e133

            <param argument="--keepCrf" type="boolean" checked="false" truevalue="--keepCrf" falsevalue="" label="CRF parameters" help="keep CRF parameters even if they are no better than HMM parameters"/>
        </section>

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