biosed.yaml

!mobyle/program
name: biosed
title: biosed
description: Replace or delete sequence sections
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:2044']
    - !mobyle/inputprogramparagraph
        prompt: Required section
        name: required
        children:
        - !mobyle/inputprogramparameter
            prompt: Sequence section to match
            format: ("", " -targetregion=" + str(value))[value is not None and value!=vdef]
            simple: true
            argpos: 2
            mandatory: true
            name: targetregion
            command: false
            type: !mobyle/stringtype {default: N}
        - !mobyle/inputprogramparameter
            prompt: Delete the target sequence sections
            format: ("", " -delete")[ bool(value) ]
            argpos: 3
            name: delete
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Replacement sequence section
            format: ("", " -replace=" + str(value))[value is not None and value!=vdef]
            argpos: 4
            name: replace
            precond: {'#not': delete}
            command: false
            type: !mobyle/stringtype {default: A}
    - !mobyle/inputprogramparagraph
        prompt: Additional section
        name: additional
        children:
        - !mobyle/inputprogramparameter
            prompt: Sequence position to match (value greater than or equal to 0)
            format: ("", " -position=" + str(value))[value is not None and value!=vdef]
            argpos: 5
            name: position
            command: false
            type: !mobyle/integertype {default: 0}
            ctrls:
            -   message: Value greater than or equal to 0 is required
                test:
                    value: {'#gte': '0'}
    - !mobyle/inputprogramparagraph
        prompt: Output section
        name: output
        children:
        - !mobyle/inputprogramparameter
            prompt: Name of the output sequence file (outseq)
            format: ("" , " -outseq=" + str(value))[value is not None]
            argpos: 6
            name: outseq
            command: false
            type: !mobyle/stringtype {default: biosed.outseq}
        - !mobyle/inputprogramparameter
            prompt: Choose the sequence output format
            format: ("", " -osformat=" + str(value))[value is not None and value!=vdef]
            argpos: 7
            name: osformat_outseq
            command: false
            type: !mobyle/stringtype
                default: FASTA
                options:
                - {label: Embl, value: EMBL}
                - {label: Fasta, value: FASTA}
                - {label: Gcg, value: GCG}
                - {label: Genbank, value: GENBANK}
                - {label: Nbrf, value: NBRF}
                - {label: Pir, value: PIR}
                - {label: Raw, value: RAW}
                - {label: Swissprot, value: SWISSPROT}
    - !mobyle/inputprogramparameter
        prompt: Turn off any prompting
        format: '" -auto -stdout"'
        argpos: 8
        name: auto
        command: false
        hidden: true
        type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparagraph
        prompt: Output section
        name: output
        children:
        - !mobyle/outputprogramparameter
            prompt: Outseq_out option
            filenames: outseq
            name: outseq_out
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"biosed.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"biosed.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0369', 'EDAM_operation:0232']
topics: ['EDAM_topic:0156']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/biosed.html', 'http://emboss.sourceforge.net/docs/themes']
command: biosed
env: {}