Mercurial > repos > rnateam > rnacommender
diff rnacommender.xml @ 0:8918de535391 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
| author | rnateam |
|---|---|
| date | Tue, 31 May 2016 05:41:03 -0400 |
| parents | |
| children | 21130153e729 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnacommender.xml Tue May 31 05:41:03 2016 -0400 @@ -0,0 +1,47 @@ +<tool id="rbc_rnacommender" name="RNAcommender" version="0.1.0"> + <description>files into a collection</description> + <requirements> + <requirement type="package" version="3.5">sam</requirement> + <requirement type="package" version="1.8.1">numpy</requirement> + <requirement type="package" version="0.17.1">pandas</requirement> + <requirement type="package" version="3.2.2">pytables</requirement> + <requirement type="package" version="0.7">theano</requirement> + <requirement type="package" version="2.10.0">requests</requirement> + </requirements> + <command detect_errors="aggressive"> + <![CDATA[ + sh $__tool_directory__/init.sh && + python $__tool_directory__/main.py "$infile" + ]]></command> + <inputs> + <param name="infile" type="data" format="fasta" label="Fasta file to split"/> + </inputs> + <outputs> + <data format="tabular" from_work_dir="output.txt" name="outfile" /> + </outputs> + <tests> + <test> + <param name="infile" value="sample.fa" /> + <output name="outfile"> + <assert_contents> + <has_text_matching expression="RBP\ttarget\ty_hat"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + RNAcommender 0.1.0 (GALAXY version). + In order to get the prediction for one (or more) RBPs, insert one fasta file with the protein sequences. The output will contain a ranked list of targets for ALL the proteins in the input file. + RNAcommender full package is available at https://github.com/gianlucacorrado/RNAcommender. + ]]></help> + <citations> + <citation type="bibtex"> + @ARTICLE{corrado2016rnacommender, + Author = {Gianluca Corrado, Toma Tebaldi, Fabrizio Costa, Paolo Frasconi and Andrea Passerini}, + keywords = {machine learning, bioinformatics, post-trainscriptional regulation, gene expression}, + title = {{RNAcommender: genome-wide recommendation of RNA-protein interactions.}}, + url = {https://github.com/gianlucacorrado/RNAcommender} + } + </citation> + </citations> +</tool>