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

Element type: slopbed

Parameters

ParameterDescriptionDefault valueParameter in Workflow FileType
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 fileout-modenumeric
Custom directory

Specify the output directory.


custom-dirstring
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.
out-namestring
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.hg18genome-idstring
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).

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

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).Falses-idboolean
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).Falsepct-idboolean
Print headerPrint the header from the input file prior to results (-header).Falseheader-idboolean

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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