Mercurial > repos > biancakrieger > nc_rna_enios
changeset 4:1831c7f4c173 draft
Uploaded
| author | biancakrieger |
|---|---|
| date | Wed, 21 Apr 2021 10:09:28 +0000 |
| parents | 84c18264a428 |
| children | d72d2ed9efac |
| files | interactions.xml |
| diffstat | 1 files changed, 21 insertions(+), 0 deletions(-) [+] |
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--- /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>