Mercurial > repos > enios > nc_rna
view riblast.xml @ 5:b2b5f193f5bd draft
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author | enios |
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date | Wed, 21 Apr 2021 10:54:52 +0000 |
parents | 3687e51201f4 |
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<tool id="riblast" name="RIBlast"> <description>"RIblast is ultrafast RNA-RNA interaction prediction software based on seed-and-extension algorithm for comprehensive lncRNA interactome analysis"</description> <requirements> <container type="docker">bianca7/riblast:latest</container> </requirements> <command><![CDATA[ RIblast db -i $inputFasta #if $optionalDb.RepeatMaskingStyle : -r $optionalDb.RepeatMaskingStyle #end if #if $optionalDb.LookupTableSize : -s $optionalDb.LookupTableSize #end if #if $optionalDb.MaximalSpan : -w $optionalDb.MaximalSpan #end if #if $optionalDb.MinAccessibleLength : -d $optionalDb.MinAccessibleLength #end if -o $outDb && set outDb1 $outDb | RIblast ris -i $InputFastaFile -d $outDb #if $optionalRis.MaxSeedLength : -l $optionalRis.MaxSeedLength #end if #if $optionalRis.HybridizationEnergyThreshold : -e $optionalRis.HybridizationEnergyThreshold #end if #if $optionalRis.InteractionEnergyThreshold : -f $optionalRis.InteractionEnergyThreshold #end if #if $optionalRis.DropOutLengthInGappedExtension : -x $optionalRis.DropOutLengthInGappedExtension #end if #if $optionalRis.DropOutLengthInUngappedExtension : -y $optionalRis.DropOutLengthInUngappedExtension #end if #if $optionalRis.OutputEnergyThreshold : -g $optionalRis.OutputEnergyThreshold #end if #if $optionalRis.OutputStyle : -s $optionalRis.OutputStyle #end if -o $outFile ]]></command> <inputs> <param type="data" name="inputFasta" format="fasta" label="Input Fasta File" /> <section name="optionalDb" title="Optional Parameters for DataBase creation" expanded="false"> <param argument="-s" name="LookupTableSize" type="integer" value="" min="1" max="100" label="Lookup table size of short string search" /> <param argument="-r" name="RepeatMaskingStyle" type="integer" value="0" min="0" max="2" label="Designation of repeat masking style 0:hard-masking, 1:soft-masking, 2:no-masking" /> <param argument="-w" name="MaximalSpan" type="integer" value="70" min="20" max="100" label="The constraint of maximal distance between the bases that form base pairs" /> <param argument="-d" name="MinAccessibleLength" type="integer" value="5" min="0" max="1000" label="Minimum accessible length for accessibility approximation " /> </section> <param type="data" name="InputFastaFile" format="fasta" label="Input Fasta File" /> <section name="optionalRis" title="Optional Parameters for Riblast" expanded="false"> <param argument="-l" name="MaxSeedLength" type="integer" value="20" min="0" max="100" label="Max size of seed length" /> <param argument="-e" name="HybridizationEnergyThreshold" type="float" value="-6.0" min="20" max="100" label="Hybridization energy threshold for seed search" /> <param argument="-f" name="InteractionEnergyThreshold" type="float" value="-4.0" min="-100" max="100" label="Interaction energy threshold for removal of the interaction candidate before gapped extension" /> <param argument="-x" name="DropOutLengthInGappedExtension" type="integer" value="16" min="0" max="1000" label="DropOut Length in gapped extension" /> <param argument="-y" name="DropOutLengthInUngappedExtension" type="integer" value="5" min="0" max="1000" label="DropOut Length in ungapped extension" /> <param argument="-g" name="OutputEnergyThreshold" type="float" value="-8.0" min="-100.0" max="100" label="Energy threshold for output" /> <param argument="-s" name="OutputStyle" type="integer" value="0" min="0" max="1" label="Designation of output format style 0:simplified output style, 1:detailed output style" /> </section> </inputs> <outputs> <data name="outDb" label="${tool.name} on ${on_string}: outDB" /> <data format="txt" name="outFile" label="${tool.name} on ${on_string}: outFile" from_work_dir="outFile"/> </outputs> </tool>