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1 <tool id="riblast" name="RIBlast">
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2 <description>"RIblast is ultrafast RNA-RNA interaction prediction software based on seed-and-extension algorithm for comprehensive lncRNA interactome analysis"</description>
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3 <requirements>
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4 <container type="docker">bianca7/riblast:latest</container>
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5 </requirements>
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6 <command><![CDATA[
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7 RIblast db -i $inputFasta
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8 #if $optionalDb.RepeatMaskingStyle :
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9 -r $optionalDb.RepeatMaskingStyle
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10 #end if
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11 #if $optionalDb.LookupTableSize :
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12 -s $optionalDb.LookupTableSize
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13 #end if
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14 #if $optionalDb.MaximalSpan :
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15 -w $optionalDb.MaximalSpan
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16 #end if
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17 #if $optionalDb.MinAccessibleLength :
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18 -d $optionalDb.MinAccessibleLength
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19 #end if
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20 -o $outDb && set outDb1 $outDb |
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21 RIblast ris
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22 -i $InputFastaFile
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23 -d $outDb
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24 #if $optionalRis.MaxSeedLength :
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25 -l $optionalRis.MaxSeedLength
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26 #end if
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27 #if $optionalRis.HybridizationEnergyThreshold :
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28 -e $optionalRis.HybridizationEnergyThreshold
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29 #end if
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30 #if $optionalRis.InteractionEnergyThreshold :
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31 -f $optionalRis.InteractionEnergyThreshold
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32 #end if
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33 #if $optionalRis.DropOutLengthInGappedExtension :
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34 -x $optionalRis.DropOutLengthInGappedExtension
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35 #end if
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36 #if $optionalRis.DropOutLengthInUngappedExtension :
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37 -y $optionalRis.DropOutLengthInUngappedExtension
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38 #end if
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39 #if $optionalRis.OutputEnergyThreshold :
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40 -g $optionalRis.OutputEnergyThreshold
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41 #end if
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42 #if $optionalRis.OutputStyle :
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43 -s $optionalRis.OutputStyle
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44 #end if
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45 -o $outFile
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46 ]]></command>
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47 <inputs>
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48 <param type="data" name="inputFasta" format="fasta" label="Input Fasta File" />
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49 <section name="optionalDb" title="Optional Parameters for DataBase creation" expanded="false">
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50 <param argument="-s" name="LookupTableSize" type="integer" value="" min="1" max="100" label="Lookup table size of short string search" />
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51 <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" />
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52 <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" />
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53 <param argument="-d" name="MinAccessibleLength" type="integer" value="5" min="0" max="1000" label="Minimum accessible length for accessibility approximation " />
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54 </section>
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55 <param type="data" name="InputFastaFile" format="fasta" label="Input Fasta File" />
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56 <section name="optionalRis" title="Optional Parameters for Riblast" expanded="false">
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57 <param argument="-l" name="MaxSeedLength" type="integer" value="20" min="0" max="100" label="Max size of seed length" />
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58 <param argument="-e" name="HybridizationEnergyThreshold" type="float" value="-6.0" min="20" max="100" label="Hybridization energy threshold for seed search" />
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59 <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" />
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60 <param argument="-x" name="DropOutLengthInGappedExtension" type="integer" value="16" min="0" max="1000" label="DropOut Length in gapped extension" />
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61 <param argument="-y" name="DropOutLengthInUngappedExtension" type="integer" value="5" min="0" max="1000" label="DropOut Length in ungapped extension" />
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62 <param argument="-g" name="OutputEnergyThreshold" type="float" value="-8.0" min="-100.0" max="100" label="Energy threshold for output" />
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63 <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" />
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64 </section>
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65 </inputs>
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66 <outputs>
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67 <data name="outDb" label="${tool.name} on ${on_string}: outDB" />
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68 <data format="txt" name="outFile" label="${tool.name} on ${on_string}: outFile" from_work_dir="outFile"/>
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69 </outputs>
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70 </tool>
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