comparison shuffleBed.xml @ 14:76e1b1b21cce default tip

Deleted selected files
author xuebing
date Tue, 13 Mar 2012 19:05:10 -0400
parents 292186c14b08
children
comparison
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13:292186c14b08 14:76e1b1b21cce
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>