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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>