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1 <tool id="interactions" name="rnaInteractions" >
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2 <requirements>
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3 <container type="docker">bianca7/lncrna:interactions</container>
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4 </requirements>
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5 <description>RNA-RNA interactions from RISE and NPINTER databases</description>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" />
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8 </stdio>
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9 <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"
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10 ]]></command>
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11 <inputs>
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12 <param format="tabular,txt" name="RNAs_file" type="data" label="differentially expressed RNA molecules (RankProd output in our lncRNA workflow)" />
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13 </inputs>
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14 <outputs>
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15 <data format="tabular" name="output1" label="Interactions' triplets (biotranslator input)"/>
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16 <data format="tabular" name="output2" label="Interactions' triplets (cytoscape input)"/>
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17 <data format="tabular" name="output3" label="mRNA reverse expressions (biotranslator input)"/>
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18 <data format="tabular" name="output4" label="mRNA reverse expressions (cytoscape input)"/>
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19 <data format="tabular" name="output5" label="RNAs not found in interactions' DBs (RiBlast input)"/>
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20 </outputs>
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21 </tool>
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