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<tool id="intarna" name="IntaRNA" version="0.1.0">
    <description></description>
    <requirements>
        <requirement type="package" version="1.2.5">intarna</requirement>
        <requirement type="package" version="1.8.5">vienna_rna</requirement>
    </requirements>
    <command>
IntaRNA
-m $query_file
-t target_file
    </command>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
    </stdio>
    <inputs>
        <param format="fasta" name="query_file" type="data" label="Query ncRNA Fasta File" />
        <param format="fasta" name="target_file" type="data" label="Target RNA Fasta File" />
        
    </inputs>
    <outputs>
        <data format="txt" name="output" label="" />
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help>**What it does**
IntaRNA is a program for the fast and accurate prediction of interactions between two RNA molecules. It has been designed to predict mRNA target sites for given non-coding RNAs (ncRNAs) like eukaryotic microRNAs (miRNAs) or bacterial small RNAs (sRNAs), but it can also be used to predict other types of RNA-RNA interactions.

Anke Busch, Andreas S. Richter, and Rolf Backofen
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
Bioinformatics, 24 no. 24 pp. 2849-56, 2008
Andreas S. Richter, Christian Schleberger, Rolf Backofen, and Claudia Steglich
Seed-based IntaRNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1
Bioinformatics, 26 no. 1 pp. 1-5, 2010

**Output**
    </help>
</tool>