Mercurial > repos > xuebing > sharplab_seq_motif
comparison mytools/shuffleBed.xml @ 0:39217fa39ff2
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| author | xuebing |
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| date | Tue, 13 Mar 2012 23:34:52 -0400 |
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| -1:000000000000 | 0:39217fa39ff2 |
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| 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> |