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comparison shuffleBed.xml @ 26:95a3b2c25bd1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
author iuc
date Thu, 26 Apr 2018 17:02:46 -0400
parents a8eabd2838f6
children 4f7a5ccd2ae9
comparison
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25:e36671a0f646 26:95a3b2c25bd1
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="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
33 <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="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="input_conditional_genome_file" /> 34 <expand macro="input_conditional_genome_file" />
35 <param name="chrom" type="boolean" checked="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)" />
104 </tests> 104 </tests>
105 <help> 105 <help>
106 <![CDATA[ 106 <![CDATA[
107 **What it does** 107 **What it does**
108 108
109 bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file. One can also provide an “exclusions” BED/GFF/VCF file that lists regions where you do not want the permuted features to be placed. For example, one might want to prevent features from being placed in known genome gaps. shuffle is useful as a null basis against which to test the significance of associations of one feature with another. 109 bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file. One can also provide an “exclusions” @STD_BEDTOOLS_INPUT_LABEL@ file that lists regions where you do not want the permuted features to be placed. For example, one might want to prevent features from being placed in known genome gaps. shuffle is useful as a null basis against which to test the significance of associations of one feature with another.
110 110
111 .. image:: $PATH_TO_IMAGES/shuffle-glyph.png 111 .. image:: $PATH_TO_IMAGES/shuffle-glyph.png
112 112
113 @REFERENCES@ 113 @REFERENCES@
114 ]]> 114 ]]>