Mercurial > repos > brigidar > getfasta
changeset 0:28c130b826a3 draft
Uploaded
| author | brigidar |
|---|---|
| date | Mon, 19 Oct 2015 20:47:17 -0400 |
| parents | |
| children | 63d8d535d834 |
| files | getfasta.xml |
| diffstat | 1 files changed, 46 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getfasta.xml Mon Oct 19 20:47:17 2015 -0400 @@ -0,0 +1,46 @@ +<tool id="bedtools_getfasta" name="extract fasta from bed" version="0.2.0"> + + <description> + </description> + + <requirements> + <requirement type="binary">bedTofasta</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> \ No newline at end of file