annotate getfasta.xml @ 0:28c130b826a3 draft

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1 <tool id="bedtools_getfasta" name="extract fasta from bed" version="0.2.0">
2     
3     <description>
4     </description>
5     
6     <requirements>
7         <requirement type="binary">bedTofasta</requirement>
8     </requirements>
9     
10     <command>
11         bedtools getfasta -fi '$input' -bed '$bedfile' -fo output.out
12     </command>
13     
14     <inputs>
15         <param format="fasta" name="input" type="data" label="fasta file from where to extract region"/>
16         <param name="bedfile" format="bed" type="data" label="bed file with regions"/>
17     </inputs>
18     
19     <outputs>
20         <data format="fasta" name="output"  from_work_dir="output.out" label="${input.name} (as fasta)"/>
21     </outputs>
22     
23     <help>
24         
25         **What it does**
26         
27         This tool converts a BED file into extracted fasta regions.
28         
29     
30         .. class:: warningmark
31         
32         This tool requires that `bedtools`__ has been installed on your system.
33         
34         ------
35         
36         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.`__
37         
38         .. __: http://code.google.com/p/bedtools/
39         .. __: http://code.google.com/p/bedtools/
40         .. __: http://cphg.virginia.edu/quinlan/
41         .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
42         
43         
44         
45     </help>
46 </tool>