cpgreport.yaml

!mobyle/program
name: cpgreport
title: cpgreport
description: Identify and report CpG-rich regions in nucleotide sequence(s)
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparagraph
        prompt: Input section
        name: input
        children:
        - !mobyle/inputprogramparameter
            prompt: Sequence option
            format: ("", " -sequence=" + str(value))[value is not None]
            simple: true
            argpos: 1
            mandatory: true
            name: sequence
            command: false
            type: !mobyle/formattedtype
                format_terms: ['EDAM_format:1927', 'EDAM_format:2200', 'EDAM_format:1935',
                    'EDAM_format:1936', 'EDAM_format:1948', 'EDAM_format:1948', 'EDAM_format:1957',
                    'EDAM_format:2188']
                data_terms: ['EDAM_data:2977']
    - !mobyle/inputprogramparagraph
        prompt: Required section
        name: required
        children:
        - !mobyle/inputprogramparameter
            comment: This sets the score for each CG sequence found. A value of 17
                is more sensitive, but 28 has also been used with some  success.
            prompt: Cpg score (value from 1 to 200)
            format: ("", " -score=" + str(value))[value is not None and value!=vdef]
            simple: true
            argpos: 2
            mandatory: true
            name: score
            command: false
            type: !mobyle/integertype {default: 17}
            ctrls:
            -   message: Value greater than or equal to 1 is required
                test:
                    value: {'#gte': '1'}
            -   message: Value less than or equal to 200 is required
                test:
                    value: {'#lte': '200'}
    - !mobyle/inputprogramparagraph
        prompt: Output section
        name: output
        children:
        - !mobyle/inputprogramparameter
            prompt: Name of the report file
            format: ("" , " -outfile=" + str(value))[value is not None]
            argpos: 3
            name: outfile
            command: false
            type: !mobyle/stringtype {default: cpgreport.outfile}
        - !mobyle/inputprogramparameter {comment: File for output features, prompt: Name
                of the output feature file (outfeat), format: '("" , " -outfeat="
                + str(value))[value is not None]', argpos: 4, name: outfeat, command: false}
        - !mobyle/inputprogramparameter {prompt: Choose the feature output format,
            format: '("", " -offormat=" + str(value))[value is not None and value!=vdef]',
            argpos: 5, name: offormat_outfeat, command: false}
    - !mobyle/inputprogramparameter
        prompt: Turn off any prompting
        format: '" -auto -stdout"'
        argpos: 6
        name: auto
        command: false
        hidden: true
        type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparagraph
        prompt: Output section
        name: output
        children:
        - !mobyle/outputprogramparameter
            prompt: Outfile_out option
            filenames: outfile
            name: outfile_out
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2048']
        - !mobyle/outputprogramparameter {prompt: Outfeat_out option, filenames: outfeat,
            name: outfeat_out}
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"cpgreport.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"cpgreport.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0430']
topics: ['EDAM_topic:0157']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/cpgreport.html', 'http://emboss.sourceforge.net/docs/themes']
command: cpgreport
env: {}