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Increases the size of each feature in files using bedtools slop.

Parameters in GUI

ParameterDescriptionDefault value
Output directorySelect an output directory. Custom - specify the output directory in the 'Custom directory' parameter. Workflow - internal workflow directory. Input file - the directory of the input file.Input file
Custom directory

Specify the output directory.

 
Output file nameA name of an output file. If default of empty value is provided the output name is the name of the first file with additional extention. 
GenomeIn order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig (-g).human.hg18
Each direction increase

Increase the BED/GFF/VCF entry by the same number base pairs in each direction. If this parameter is used -l and -l are ignored. Enter 0 to disable (-b).

0
Substract from startThe number of base pairs to subtract from the start coordinate. Enter 0 to disable (-l).0
Add to endThe number of base pairs to add to the end coordinate. Enter 0 to disable (-r).0

Strand-based

Define -l and -r based on strand. For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate (-s).False
As fractionDefine -l and -r as a fraction of the feature’s length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstreamâ (-pct).False
Print headerPrint the header from the input file prior to results (-header).False

Parameters in Workflow File 

Type: slopbed

ParameterParameter in the GUIType
out-modeOutput directorynumeric
custom-dirCustom directorystring
out-nameOutput file namestring
genome-idGenomestring
b-idEach direction increasenumeric
l-idSubstract from startnumeric
r-idAdd to endnumeric
s-idStrand-basedboolean
pct-idAs fractionboolean
header-idPrint headerboolean

Input/Output Ports

The element has 1 input port:

Name in GUI: Input File

Name in Workflow File: in-file

Slots:

Slot In GUISlot in Workflow FileType
Source URLurlstring

And 1 output port:

Name in GUI: Output File

Name in Workflow File: out-file

Slots:

Slot In GUISlot in Workflow FileType
Source URLurlstring
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