# HG changeset patch
# User brigidar
# Date 1445302037 14400
# Node ID 28c130b826a3fff206addffa37e06048b25fe5ce

Uploaded

diff -r 000000000000 -r 28c130b826a3 getfasta.xml
--- /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>
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