Mercurial > repos > xuebing > sharplabtool
diff mytools/shuffleBed.xml @ 7:f0dc65e7f6c0
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author | xuebing |
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date | Fri, 09 Mar 2012 19:59:07 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mytools/shuffleBed.xml Fri Mar 09 19:59:07 2012 -0500 @@ -0,0 +1,43 @@ +<tool id="shufflebed" name="shuffleBed"> + <description>chromosome not weighted by length</description> + <command>shuffleBed -i $input -g $genome $chrom > $outfile + #if $limit.limit_select=="include": + -incl $limitfile + #else if $limit.limit_select=="exclude": + -excl $limitfile + #end if + </command> + <inputs> + <param name="input" format="bed,gff,vcf" type="data" label="Original intervals (BED/GFF/VCF)" /> + <param name="genome" type="select" label="Select genome"> + <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option> + <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option> + <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option> + <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option> + </param> + <param name="chrom" label="keep intervals on the same chromosome?" type="boolean" truevalue="-chrom" falsevalue="" checked="False"/> + <conditional name="limit"> + <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)."> + <option value="none" selected="true">None</option> + <option value="include">within specified regions</option> + <option value="exclude">outside specified regions</option> + </param> + <when value="include"> + <param name="limitfile" type="data" format="interval" label="specify regions"/> + </when> + <when value="exclude"> + <param name="limitfile" type="data" format="interval" label="specify regions"/> + </when> + </conditional> + </inputs> + <outputs> + <data format="input" name="outfile" /> + </outputs> + <help> + +.. class:: infomark + +Every chromosome are choosed with equal probability, regardless their size. Please use the tool 'random intervals' instead for general randomization. + + </help> +</tool>