Slopbed Element

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

Element type: slopbed

Parameter	Description	Default value	Parameter in Workflow File	Type
Output directory	Select 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
out-mode	numeric
Custom directory	Specify the output directory.		custom-dir	string
Output file name	A name of an output file. If a default or empty value is provided, the output name is the name of the first file with an additional extension.		out-name	string
Genome	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	genome-id	string
Each direction increase	Increase the BED/GFF/VCF entry by the same number of base pairs in each direction. If this parameter is used, -l and -r are ignored. Enter 0 to disable (-b).	0	b-id	numeric
Subtract from start	The number of base pairs to subtract from the start coordinate. Enter 0 to disable (-l).	0	l-id	numeric
Add to end	The number of base pairs to add to the end coordinate. Enter 0 to disable (-r).	0	r-id	numeric
Strand-based	Define -l and -r based on strand. For example, if used, -l 500 for a negative-stranded feature will add 500 bp to the end coordinate (-s).	False	s-id	boolean
As fraction	Define -l and -r as a fraction of the feature’s length. E.g., if used on a 1000 bp feature, -l 0.50, will add 500 bp upstream (-pct).	False	pct-id	boolean
Print header	Print the header from the input file prior to results (-header).	False	header-id	boolean

Input/Output Ports

The element has 1 input port:

Name in GUI: Input File

Name in Workflow File: in-file

Slots:

Slot In GUI	Slot in Workflow File	Type
Source URL	url	string

And 1 output port:

Name in GUI: Output File

Name in Workflow File: out-file

Slots:

Slot In GUI	Slot in Workflow File	Type
Source URL	url	string