Mercurial > repos > brigidar > getfasta

<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>
author	brigidar
date	Tue, 20 Oct 2015 21:34:42 -0400
parents	63d8d535d834
children