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comparison braker3.xml @ 2:bbe51a1c2b6b draft

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planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit 791a8381ca30aeb8222e2e43f9119f34a040224b
author genouest
date Tue, 24 Oct 2023 12:24:40 +0000
parents bd103884a09c
children 5460380cc057
comparison
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1:bd103884a09c 2:bbe51a1c2b6b
46 $augustus.crf 46 $augustus.crf
47 --rounds $augustus.rounds 47 --rounds $augustus.rounds
48 $augustus.AUGUSTUS_ab_initio 48 $augustus.AUGUSTUS_ab_initio
49 $augustus.keepCrf 49 $augustus.keepCrf
50 50
51 $advanced.UTR 51 ##$advanced.UTR
52 52
53 $advanced.filterOutShort 53 $advanced.filterOutShort
54 54
55 #if $advanced.eval: 55 #if $advanced.eval:
56 --eval ${advanced.eval} 56 --eval ${advanced.eval}
108 <param argument="--AUGUSTUS_ab_initio" type="boolean" checked="false" truevalue="--AUGUSTUS_ab_initio" falsevalue="" label="Output ab initio predictions by AUGUSTUS"/> 108 <param argument="--AUGUSTUS_ab_initio" type="boolean" checked="false" truevalue="--AUGUSTUS_ab_initio" falsevalue="" label="Output ab initio predictions by AUGUSTUS"/>
109 <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"/> 109 <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"/>
110 </section> 110 </section>
111 111
112 <section name="advanced" expanded="false" title="Advanced"> 112 <section name="advanced" expanded="false" title="Advanced">
113 <param argument="--UTR" type="boolean" checked="false" truevalue="--UTR=on" falsevalue="" label="" help="Experimental, requires RNASeq data (bam) and a softmasked genome" /> 113 <!--param argument="-\-UTR" type="boolean" checked="false" truevalue="-\-UTR=on" falsevalue="" label="" help="Experimental, requires RNASeq data (bam) and a softmasked genome" /-->
114 <param argument="--filterOutShort" type="boolean" checked="false" truevalue="--filterOutShort" falsevalue="" label="Filter out too short traingin gene predicted by GeneMark-EX" /> 114 <param argument="--filterOutShort" type="boolean" checked="false" truevalue="--filterOutShort" falsevalue="" label="Filter out too short traingin gene predicted by GeneMark-EX" />
115 <param argument="--eval" type="data" format="gtf" optional="true" label="Reference set to evaluate predictions" help="using evaluation scripts from GaTech" /> 115 <param argument="--eval" type="data" format="gtf" optional="true" label="Reference set to evaluate predictions" help="using evaluation scripts from GaTech" />
116 <param argument="--eval_pseudo" type="data" format="gff3" optional="true" label="File with pseudogenes that will be excluded from accuracy evaluation" /> 116 <param argument="--eval_pseudo" type="data" format="gff3" optional="true" label="File with pseudogenes that will be excluded from accuracy evaluation" />
117 <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"/> 117 <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"/>
118 </section> 118 </section>