Increases the size of each feature in files using bedtools slop.
Element type: slopbed
Parameters
| 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 default of empty value is provided the output name is the name of the first file with additional extention. | out-name | string | |
| Genome | In 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 | genome-id | string |
| 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 | b-id | numeric |
| Substract 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, it will add 500 bp to the end coordinate (-s). | False | s-id | boolean |
| As fraction | Define -l and -r as a fraction of the featureâs length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp âupstreamâ (-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 |