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