# HG changeset patch
# User biancakrieger
# Date 1618999768 0
# Node ID 1831c7f4c1738409ff4eb6545f6f4d7b2f7e9d4b
# Parent  84c18264a42858ec28ce5508b8925904b4d0c746
Uploaded

diff -r 84c18264a428 -r 1831c7f4c173 interactions.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/interactions.xml	Wed Apr 21 10:09:28 2021 +0000
@@ -0,0 +1,21 @@
+<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>