Tool produces GFF output from the file generated by iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl tool Both islands_file and islands_control_file should be produced by the same tool

-b and -c arguments are not supported

Tool sorts data from `unsorted_file` by key

`default_output_filename` function returns file name identical to `unsorted_file`, if `output_filename` is not provided.

Tool renames `source_file` to `target_filename`. Input `target_filename` should be set as string. If it's a full path, only basename will be used. If BAI file is present, it will be renamed too

Tool to run custom script set as `script` input with arguments from `param`. Default script runs sed command over the input file and exports results to the file with the same name as input's basename

Tool assigns each peak obtained from MACS2 to a gene and region (upstream, promoter, exon, intron, intergenic)

`default_output_filename` function returns output filename with sufix set as `ext` argument. Function is called when either `output_filename` or `log_filename` inputs are not provided.

Tool converts bed file to bigBed

Before running `baseCommand` the following files are created in Docker working directory (using `InitialWorkDirRequirement`): `narrowpeak.as` - default BED file structure template for ENCODE narrowPeak format `broadpeak.as` - default BED file structure template for ENCODE broadPeak format

`default_output_filename` function returns default output file name based on `input_bed` basename with `*.bb` extension if `output_filename` is not provided.

`get_bed_type` function returns default BED file type if `bed_type` is not provided. Depending on `input_bed` file extension the following values are returned: `*.narrowpeak` --> bed6+4 `*.broadpeak` --> bed6+3 else --> null (`bedToBigBed` will use its own default value)

`get_bed_template` function returns default BED file template if `bed_template` is not provided. Depending on `input_bed` file extension the following values are returned: `*.narrowpeak` --> narrowpeak.as (previously staged into Docker working directory) `*.broadpeak` --> broadpeak.as (previously staged into Docker working directory) else --> null (`bedToBigBed` will use its own default value)

Tool to run custom script set as `script` input with arguments from `param`. Default script runs sed command over the input file and exports results to the file with the same name as input's basename