comparison shuffleBed.xml @ 26:95a3b2c25bd1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59

25:e36671a0f646

        -maxTries $maxtries
        > '$output'
]]>
    </command>
    <inputs>
        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
        <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" />
        <expand macro="input_conditional_genome_file" />
        <param name="chrom" type="boolean" checked="False" truevalue="-chrom" falsevalue=""
            label="Keep features in the input file on the same chromosome"
            help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen. (-chrom)" />

    </tests>
    <help>
<![CDATA[
**What it does**

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.

.. image:: $PATH_TO_IMAGES/shuffle-glyph.png

@REFERENCES@
]]>

26:95a3b2c25bd1

        -maxTries $maxtries
        > '$output'
]]>
    </command>
    <inputs>
        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" />
        <expand macro="input_conditional_genome_file" />
        <param name="chrom" type="boolean" checked="False" truevalue="-chrom" falsevalue=""
            label="Keep features in the input file on the same chromosome"
            help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen. (-chrom)" />

    </tests>
    <help>
<![CDATA[
**What it does**

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.

.. image:: $PATH_TO_IMAGES/shuffle-glyph.png

@REFERENCES@
]]>