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comparison shuffleBed.xml @ 26:c0fbce5dc84a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
author iuc
date Mon, 17 Oct 2016 10:13:20 -0400
parents ac8b17b66663
children b0d5e752c0c5
comparison
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25:6c6963cf9136 26:c0fbce5dc84a
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 bedtools shuffle 10 bedtools shuffle
11 -g $genome 11 -g '$genome'
12 -i $inputA 12 -i '$inputA'
13 $bedpe 13 $bedpe
14 #if str($seed.seed_choose) == "True": 14 #if str($seed.seed_choose) == "True":
15 -seed $seed.seed 15 -seed $seed.seed
16 #end if 16 #end if
17 #if str($add_bed.add_bed_select) == "not_be": 17 #if str($add_bed.add_bed_select) == "not_be":
23 $chrom 23 $chrom
24 $chromfirst 24 $chromfirst
25 $no_overlap 25 $no_overlap
26 $allow_beyond 26 $allow_beyond
27 -maxTries $maxtries 27 -maxTries $maxtries
28 > $output 28 > '$output'
29 ]]> 29 ]]>
30 </command> 30 </command>
31 <inputs> 31 <inputs>
32 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> 32 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
33 <param name="bedpe" type="boolean" label="The file is in BEDPE format" selected="False" truevalue="-bedpe" falsevalue="" /> 33 <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" />
34 <expand macro="genome" /> 34 <expand macro="genome" />
35 <param name="chrom" type="boolean" selected="False" truevalue="-chrom" falsevalue="" 35 <param name="chrom" type="boolean" checked="False" truevalue="-chrom" falsevalue=""
36 label="Keep features in the input file on the same chromosome" 36 label="Keep features in the input file on the same chromosome"
37 help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen. (-chrom)" /> 37 help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen. (-chrom)" />
38 <expand macro="seed" /> 38 <expand macro="seed" />
39 <conditional name="add_bed"> 39 <conditional name="add_bed">
40 <param name="add_bed_select" type="select" label="Choose an additional BED file"> 40 <param name="add_bed_select" type="select" label="Choose an additional BED file">
49 </when> 49 </when>
50 <when value="be"> 50 <when value="be">
51 <param name="incl" type="data" format="bed" label="Choose File" /> 51 <param name="incl" type="data" format="bed" label="Choose File" />
52 </when> 52 </when>
53 </conditional> 53 </conditional>
54 <param name="chromfirst" type="boolean" selected="False" truevalue="-chromFirst" falsevalue="" 54 <param name="chromfirst" type="boolean" checked="False" truevalue="-chromFirst" falsevalue=""
55 label="Choose chromosome first" 55 label="Choose chromosome first"
56 help="Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size. (-chromFirst)" /> 56 help="Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size. (-chromFirst)" />
57 <param name="maxtries" type="integer" value="1000" 57 <param name="maxtries" type="integer" value="1000"
58 label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" help="(-maxTries)" /> 58 label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" help="(-maxTries)" />
59 <param name="no_overlap" type="boolean" selected="False" truevalue="-noOverlapping" falsevalue="" 59 <param name="no_overlap" type="boolean" checked="False" truevalue="-noOverlapping" falsevalue=""
60 label="Don’t allow shuffled intervals to overlap" help="(-noOverlapping)" /> 60 label="Don’t allow shuffled intervals to overlap" help="(-noOverlapping)" />
61 <param name="allow_beyond" type="boolean" selected="False" truevalue="-allowBeyondChromEnd" falsevalue="" 61 <param name="allow_beyond" type="boolean" checked="False" truevalue="-allowBeyondChromEnd" falsevalue=""
62 label="Allow the original the length of the original records to extebd beyond the length of the chromosome" help="(-allowBeyondChromEnd)" /> 62 label="Allow the original the length of the original records to extebd beyond the length of the chromosome" help="(-allowBeyondChromEnd)" />
63 </inputs> 63 </inputs>
64 <outputs> 64 <outputs>
65 <data format="bed" name="output" /> 65 <data format="bed" name="output" />
66 </outputs> 66 </outputs>