<tool id="interactions" name="rnaInteractions" >
 <requirements>
     <container type="docker">bianca7/lncrna:interactions</container>
 </requirements>
 <description>RNA-RNA interactions from RISE and NPINTER databases</description>
 <stdio>
   <exit_code range="1:" level="fatal" />
 </stdio>
 <command><![CDATA[ Rscript /code/interactions.R $RNAs_file && cp bim_triplnetwork.tsv "$output1" && cp cs_triplnetwork.tsv "$output2" && cp bim_mRNAtarget.tsv "$output3" && cp cs_mRNAtarget.tsv "$output4" && cp not_found_interactions.tsv "$output5"
  ]]></command>
  <inputs>
   <param format="tabular,txt" name="RNAs_file" type="data" label="differentially expressed RNA molecules (RankProd output in our lncRNA workflow)" />
 </inputs>
 <outputs>
    <data format="tabular" name="output1" label="Interactions' triplets (biotranslator input)"/>
    <data format="tabular" name="output2" label="Interactions' triplets (cytoscape input)"/>
    <data format="tabular" name="output3" label="mRNA reverse expressions (biotranslator input)"/>
    <data format="tabular" name="output4" label="mRNA reverse expressions (cytoscape input)"/>
    <data format="tabular" name="output5" label="RNAs not found in interactions' DBs (RiBlast input)"/>
 </outputs>
</tool>