annotateBed_2.15.0.yaml

!mobyle/program
name: annotateBed
version: 2.15.0
title: 'BEDtools: Annotate BED files'
description: annotateBed annotates a BED/VCF/GFF file with the coverage and number
    of overlaps observed from multiple other BED/VCF/GFF files. In this way, it allows
    one to ask to what degree one feature coincides with multiple other feature types
    with a single command.
authors: Quinlan A.R. & Hall I.M.
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparagraph
        prompt: Input
        name: input_para
        children:
        - !mobyle/inputprogramparameter
            comment: BED/VCF/GFF format file that should be used as the basis of comparing
                the annotation
            prompt: BED/VCF/GFF data that needs annotation (-i)
            format: '" -i " + str( value )'
            simple: true
            argpos: 50
            mandatory: true
            name: input_file
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/inputprogramparameter
            comment: Data should be BED/VCF/GFF format file. If multiple files are
                to be compared then upload a zip file or tar.gz file using the upload
                option.
            prompt: Data used for comparison
            format: '" -files " + str( value )'
            simple: true
            argpos: 51
            mandatory: true
            name: input_other_files
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
    - !mobyle/inputprogramparagraph
        prompt: Options
        name: options_para
        children:
        - !mobyle/inputprogramparameter
            comment: List of names (one per file uploaded). These names will be printed
                as a header line.
            prompt: List of names that corresponds to the uploaded files (-names)
            format: ("", " -names " + str(value))[value is not None]
            name: file_names
            command: false
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            comment: "Default option: overlaps are counted without respect to strand.Same\
                \ strandedness option: only counts overlaps on the _same_ strand.Different\
                \ strandedness option: only count overlaps \ton the _opposite_ strand."
            prompt: Strandedness (-s or -S)
            format: ("", " " + str(value))[value is not None and value!=vdef]
            argpos: 3
            name: force_strand_option
            command: false
            type: !mobyle/stringtype
                default: ignore
                options:
                - {label: Ignore strandedness (default), value: ignore}
                - {label: Same strandedness, value: -s}
                - {label: Different strandedness, value: -S}
    - !mobyle/inputprogramparagraph
        prompt: Output
        name: output_para
        argpos: 8
        children:
        - !mobyle/inputprogramparameter
            prompt: 'Enter output file prefix:'
            format: (" > " + str(vdef) , " > " + str(value))[value is not None] +
                ".bed"
            simple: true
            argpos: 52
            mandatory: true
            name: output_file
            command: false
            type: !mobyle/stringtype {default: annotated_data}
        - !mobyle/inputprogramparameter
            prompt: Report options (-counts or -both)
            format: ("" , "  " +  str(value))[value is not None and value != vdef]
            name: report_options
            command: false
            type: !mobyle/stringtype
                default: frac
                options:
                - {label: Only % coverage of the first file with each of the other
                        files, value: frac}
                - {label: Only counts of the first file with each of the other files,
                    value: -counts}
                - {label: Both counts and % coverage, value: -both}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparagraph
        prompt: Output
        name: output_para
        argpos: 8
        children:
        - !mobyle/outputprogramparameter
            prompt: GenomeAnnotation
            filenames: ("annotated_data",output_file)[output_file is not None] + ".bed"
            name: annotateBed_out
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"annotateBed.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"annotateBed.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:3194']
topics: ['EDAM_topic:0160']
command: annotateBed
env: {}