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bedtools ShuffleBed tool metadata

Miscellaneous

Name: bedtools ShuffleBed

Description: randomly redistrubute intervals in a genome

Id: bedtools_shufflebed

Guid: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1

Version: 2.30.0+galaxy1

Version command string: bedtools --version

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0

toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.29.2

toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.19.0

bedtools_shufflebed

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

bedtools

2.30.0

package

Additional information about this tool

Command:

bedtools shuffle

#if $genome_file_opts.genome
    -g 
    #if $genome_file_opts.genome_file_opts_selector == "loc":
        '$genome_file_opts.genome.fields.len_path'
    #elif $genome_file_opts.genome_file_opts_selector == "hist":
        '$genome_file_opts.genome'
    #end if
#end if
    
-i '$inputA'
$bedpe
#if str($seed.seed_choose) == "True":
    -seed $seed.seed
#end if
#if str($add_bed.add_bed_select) == "not_be":
    -excl $add_bed.excl
    #if str($add_bed.overlap)
        -f $add_bed.overlap
    #end if
#elif str($add_bed.add_bed_select) == "be":
    -incl $add_bed.incl
#end if
$chrom
$chromfirst
$no_overlap
$allow_beyond
-maxTries $maxtries
> '$output'

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

inputA: shuffleBed1.bed
genome_file_opts|genome: shuffleBed.len
genome_file_opts|genome_file_opts_selector: hist
chrom: False
seed|seed: 1
seed|seed_choose: True

name: value

shuffleBed1.bed
shuffleBed.len
value

Test-2

inputA: shuffleBed1.bed
genome_file_opts|genome: shuffleBed.len
genome_file_opts|genome_file_opts_selector: hist
chrom: True
seed|seed: 1
seed|seed_choose: True

name: value

shuffleBed1.bed
shuffleBed.len
value

Test-3

name: value

shuffleBed1.bed
shuffleBed.len
shuffleBed2.bed
value

Test-4

inputA: shuffleBed1.bed
genome_file_opts|genome: shuffleBed.len
genome_file_opts|genome_file_opts_selector: hist
seed|seed: 3
seed|seed_choose: True
allow_beyond: True

name: value

shuffleBed1.bed
shuffleBed.len
value