--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mytools/shuffleBed.xml	Fri Mar 09 20:01:43 2012 -0500
@@ -0,0 +1,43 @@
+<tool id="shufflebed" name="shuffleBed">
+  <description>chromosome not weighted by length</description>
+  <command>shuffleBed -i $input -g $genome $chrom > $outfile 
+    #if $limit.limit_select=="include":
+    -incl $limitfile
+    #else if $limit.limit_select=="exclude":
+    -excl $limitfile 
+    #end if
+  </command>
+  <inputs>
+    <param name="input" format="bed,gff,vcf" type="data" label="Original intervals (BED/GFF/VCF)" />
+    <param name="genome" type="select" label="Select genome">
+     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option>
+     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option>
+     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option>
+     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option>
+    </param>
+    <param name="chrom" label="keep intervals on the same chromosome?" type="boolean" truevalue="-chrom" falsevalue="" checked="False"/>
+    <conditional name="limit">
+    	<param name="limit_select" type="select" label="restrictions for the shuffling" help="Instead of randomly placing features in a genome, one can specify regions features should or should not be randomly placed (e.g. genes.bed or repeats.bed).">
+		<option value="none" selected="true">None</option>
+		<option value="include">within specified regions</option>
+		<option value="exclude">outside specified regions</option>
+	    </param>
+	    <when value="include">
+		    <param name="limitfile" type="data" format="interval" label="specify regions"/>
+	    </when>
+	    <when value="exclude">
+		    <param name="limitfile" type="data" format="interval" label="specify regions"/>
+	    </when>
+    </conditional>         
+  </inputs>
+  <outputs>
+    <data format="input" name="outfile" />
+  </outputs>
+  <help>
+  
+.. class:: infomark
+
+Every chromosome are choosed with equal probability, regardless their size. Please use the tool 'random intervals' instead for general randomization.
+
+  </help>
+</tool>