| Previous changeset 0:d445743c65bf (2012-03-31) Next changeset 2:7676fe4566a6 (2012-03-31) |
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added:
bed_shuffle.xml |
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| diff -r d445743c65bf -r bac957616de7 bed_shuffle.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bed_shuffle.xml Sat Mar 31 13:58:45 2012 -0400 |
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| @@ -0,0 +1,44 @@ +<tool id="bed_shuffle" name="bed_shuffle"> + <description>shuffle intervals 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 chromsome size file" > + <options from_file="chrsize.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </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> |