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Parameter | Description | Default value |
---|---|---|
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 |
Custom directory | Specify the output directory. | |
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. | |
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 |
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 start | The number of base pairs to subtract from the start coordinate. Enter 0 to disable (-l). | 0 |
Add to end | The 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 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 |
Print header | Print the header from the input file prior to results (-header). | False |
Parameters in Workflow File
Type: slopbed
Parameter | Parameter in the GUI | Type |
---|---|---|
out-mode | Output directory | numeric |
custom-dir | Custom directory | string |
out-name | Output file name | string |
genome-id | Genome | string |
b-id | Each direction increase | numeric |
l-id | Substract from start | numeric |
r-id | Add to end | numeric |
s-id | Strand-based | boolean |
pct-id | As fraction | boolean |
header-id | Print header | boolean |
Input/Output Ports
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