--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/shuffleBed.xml	Tue Nov 04 01:45:04 2014 -0500
@@ -0,0 +1,68 @@
+<tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+        bedtools shuffle
+        -g $genome
+        -i $inputA
+        $bedpe
+        #if $seed.choose:
+        -seed $seed.seed
+        #end if
+        #if $excl.choose:
+        -excl $excl.excl
+        -f $overlap
+        #end if
+         #if $incl.choose:
+        -incl $incl.incl
+        #end if
+        $chrom
+        $chromfirst
+        $nooverlap
+        $allowBeyond
+        -maxTries $maxtries
+        &gt; $output
+    </command>
+    <inputs>
+        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
+        <param name="bedpe" type="boolean" label="The file is in BEDPE format" selected="False" truevalue="-bedpe" falsevalue="" />
+        <expand macro="genome" />
+        <param name="chrom" type="boolean" label="Keep features in the input file on the same chromosome. Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen" selected="False" truevalue="-chrom" falsevalue="" />
+        <expand macro="seed" />
+        <conditional name="excl">
+            <param name="choose" type="boolean" label="Choose a BED file of coordinates in which features from -i should not be placed?" selected="False" truevalue="True" falsevalue="False" />
+            <when value="True">
+                <param name="excl" type="data" format="bed" label="Choose File" />
+                <expand macro="overlap" />
+            </when>
+        </conditional>
+        <conditional name="incl">
+            <param name="choose" type="boolean" label="Choose a BED file of coordinates in which features from -i should be placed?" selected="False" truevalue="True" falsevalue="False" />
+            <when value="True">
+                <param name="incl" type="data" format="bed" label="Choose File" />
+            </when>
+        </conditional>
+        
+        <param name="chromfirst" type="boolean" selected="False" truevalue="-chromFirst" falsevalue="" 
+            label="Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size" />
+        <param name="maxtries" type="integer" value="1000" label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" />
+        <param name="nooverlap" type="boolean" selected="False" truevalue="-noOverlapping" falsevalue="" label="Don’t allow shuffled intervals to overlap" />
+        <param name="allowBeyond" type="boolean" selected="False" truevalue="-allowBeyondChromEnd" falsevalue="" label="Allow the original the length of the original records to extebd beyond the length of the chromosome." />
+    </inputs>
+    <outputs>
+        <data format="bed" name="output" />
+    </outputs>
+    <help>
+
+**What it does**
+
+bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file. One can also provide an “exclusions” BED/GFF/VCF file that lists regions where you do not want the permuted features to be placed. For example, one might want to prevent features from being placed in known genome gaps. shuffle is useful as a null basis against which to test the significance of associations of one feature with another.
+.. image:: $PATH_TO_IMAGES/shuffle-glyph.png
+@REFERENCES@
+    </help>
+    <expand macro="citations" />
+</tool>