<tool id="rbc_rnacommender" name="RNAcommender" version="0.1.1">
    <description>genome-wide recommendation of RNA-protein interactions</description>
    <requirements>
        <requirement type="package" version="3.5">sam</requirement>
        <requirement type="package" version="1.11.1">numpy</requirement>
        <requirement type="package" version="0.17.1">scipy</requirement>
        <requirement type="package" version="0.18.1">pandas</requirement>
        <requirement type="package" version="3.2.2">pytables</requirement>
        <requirement type="package" version="0.8.2">theano</requirement>
        <requirement type="package" version="2.10.0">requests</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>
    <command>
    <![CDATA[
        sh $__tool_directory__/init.sh 2> hide.txt &&
        THEANO_FLAGS=base_compiledir=./tmp python $__tool_directory__/main.py "$infile"
    ]]></command>
    <inputs>
        <param name="infile" type="data" format="fasta" label="Fasta file containing (exactly) one RBP sequence"/>
    </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>