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1 <tool id="bed_shuffle" name="bed_shuffle">
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2 <description>shuffle intervals 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 chromsome size file" >
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13 <options from_file="chrsize.loc">
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14 <column name="name" index="0"/>
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15 <column name="value" index="1"/>
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16 </options>
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17 </param>
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18
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19 <param name="chrom" label="keep intervals on the same chromosome?" type="boolean" truevalue="-chrom" falsevalue="" checked="False"/>
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20 <conditional name="limit">
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21 <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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22 <option value="none" selected="true">None</option>
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23 <option value="include">within specified regions</option>
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24 <option value="exclude">outside specified regions</option>
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25 </param>
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26 <when value="include">
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27 <param name="limitfile" type="data" format="interval" label="specify regions"/>
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28 </when>
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29 <when value="exclude">
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30 <param name="limitfile" type="data" format="interval" label="specify regions"/>
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31 </when>
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32 </conditional>
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33 </inputs>
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34 <outputs>
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35 <data format="input" name="outfile" />
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36 </outputs>
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37 <help>
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38
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39 .. class:: infomark
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40
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41 Every chromosome are choosed with equal probability, regardless their size. Please use the tool 'random intervals' instead for general randomization.
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42
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43 </help>
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44 </tool>
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