<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>
