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<tool id="bedtools_getfasta" name="extract fasta from bed" version="0.3.0">
    
    <description>
    </description>
    
    <requirements>
        <requirement type="package" version="2.22">bedtools</requirement>
    </requirements>
    
    <command>
        bedtools getfasta -fi '$input' -bed '$bedfile' -fo output.out
    </command>
    
    <inputs>
        <param format="fasta" name="input" type="data" label="fasta file from where to extract region"/>
        <param name="bedfile" format="bed" type="data" label="bed file with regions"/>
    </inputs>
    
    <outputs>
        <data format="fasta" name="output"  from_work_dir="output.out" label="${input.name} (as fasta)"/>
    </outputs>
    
    <help>
        
        **What it does**
        
        This tool converts a BED file into extracted fasta regions.
        
    
        .. class:: warningmark
        
        This tool requires that `bedtools`__ has been installed on your system.
        
        ------
        
        This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
        
        .. __: http://code.google.com/p/bedtools/
        .. __: http://code.google.com/p/bedtools/
        .. __: http://cphg.virginia.edu/quinlan/
        .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
        
        
        
    </help>
</tool>