# HG changeset patch
# User enios
# Date 1619002471 0
# Node ID 3687e51201f4a7a974b815756f74e00009e7b26c
# Parent  e3546c89d20ed366537b9dde3c7194968aa022ae
Uploaded

diff -r e3546c89d20e -r 3687e51201f4 riblast.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/riblast.xml	Wed Apr 21 10:54:31 2021 +0000
@@ -0,0 +1,70 @@
+<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>