Mercurial > repos > xuebing > bed_shuffle
comparison bed_shuffle.xml @ 1:bac957616de7
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| author | xuebing |
|---|---|
| date | Sat, 31 Mar 2012 13:58:45 -0400 |
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| children |
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| 0:d445743c65bf | 1:bac957616de7 |
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| 1 <tool id="bed_shuffle" name="bed_shuffle"> | |
| 2 <description>shuffle intervals 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 chromsome size file" > | |
| 13 <options from_file="chrsize.loc"> | |
| 14 <column name="name" index="0"/> | |
| 15 <column name="value" index="1"/> | |
| 16 </options> | |
| 17 </param> | |
| 18 | |
| 19 <param name="chrom" label="keep intervals on the same chromosome?" type="boolean" truevalue="-chrom" falsevalue="" checked="False"/> | |
| 20 <conditional name="limit"> | |
| 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)."> | |
| 22 <option value="none" selected="true">None</option> | |
| 23 <option value="include">within specified regions</option> | |
| 24 <option value="exclude">outside specified regions</option> | |
| 25 </param> | |
| 26 <when value="include"> | |
| 27 <param name="limitfile" type="data" format="interval" label="specify regions"/> | |
| 28 </when> | |
| 29 <when value="exclude"> | |
| 30 <param name="limitfile" type="data" format="interval" label="specify regions"/> | |
| 31 </when> | |
| 32 </conditional> | |
| 33 </inputs> | |
| 34 <outputs> | |
| 35 <data format="input" name="outfile" /> | |
| 36 </outputs> | |
| 37 <help> | |
| 38 | |
| 39 .. class:: infomark | |
| 40 | |
| 41 Every chromosome are choosed with equal probability, regardless their size. Please use the tool 'random intervals' instead for general randomization. | |
| 42 | |
| 43 </help> | |
| 44 </tool> |