20
+ − 1 <tool id="shufflebed" name="shuffleBed">
+ − 2 <description>chromosome not weighted by length</description>
+ − 3 <command>shuffleBed -i $input -g $genome $chrom > $outfile
+ − 4 #if $limit.limit_select=="include":
+ − 5 -incl $limitfile
+ − 6 #else if $limit.limit_select=="exclude":
+ − 7 -excl $limitfile
+ − 8 #end if
+ − 9 </command>
+ − 10 <inputs>
+ − 11 <param name="input" format="bed,gff,vcf" type="data" label="Original intervals (BED/GFF/VCF)" />
+ − 12 <param name="genome" type="select" label="Select genome">
+ − 13 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option>
+ − 14 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option>
+ − 15 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option>
+ − 16 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option>
+ − 17 </param>
+ − 18 <param name="chrom" label="keep intervals on the same chromosome?" type="boolean" truevalue="-chrom" falsevalue="" checked="False"/>
+ − 19 <conditional name="limit">
+ − 20 <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).">
+ − 21 <option value="none" selected="true">None</option>
+ − 22 <option value="include">within specified regions</option>
+ − 23 <option value="exclude">outside specified regions</option>
+ − 24 </param>
+ − 25 <when value="include">
+ − 26 <param name="limitfile" type="data" format="interval" label="specify regions"/>
+ − 27 </when>
+ − 28 <when value="exclude">
+ − 29 <param name="limitfile" type="data" format="interval" label="specify regions"/>
+ − 30 </when>
+ − 31 </conditional>
+ − 32 </inputs>
+ − 33 <outputs>
+ − 34 <data format="input" name="outfile" />
+ − 35 </outputs>
+ − 36 <help>
+ − 37
+ − 38 .. class:: infomark
+ − 39
+ − 40 Every chromosome are choosed with equal probability, regardless their size. Please use the tool 'random intervals' instead for general randomization.
+ − 41
+ − 42 </help>
+ − 43 </tool>
