backtranambig.yaml

!mobyle/program
name: backtranambig
title: backtranambig
description: Back-translate a protein sequence to ambiguous nucleotide sequence
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:2976']
    - !mobyle/inputprogramparagraph
        prompt: Additional section
        name: additional
        children:
        - !mobyle/inputprogramparameter
            prompt: Genetic codes
            format: ("", " -table=" + str(value))[value is not None and value!=vdef]
            argpos: 2
            name: table
            command: false
            type: !mobyle/stringtype
                default: '0'
                options:
                - {label: Standard, value: '0'}
                - {label: Standard (with alternative initiation codons), value: '1'}
                - {label: Vertebrate mitochondrial, value: '2'}
                - {label: Yeast mitochondrial, value: '3'}
                - {label: 'Mold, protozoan, coelenterate mitochondrial and  mycoplasma/spiroplasma',
                    value: '4'}
                - {label: Invertebrate mitochondrial, value: '5'}
                - {label: Ciliate  macronuclear and dasycladacean, value: '6'}
                - {label: Echinoderm mitochondrial, value: '9'}
                - {label: Euplotid nuclear, value: '10'}
                - {label: Bacterial, value: '11'}
                - {label: Alternative yeast nuclear, value: '12'}
                - {label: Ascidian mitochondrial, value: '13'}
                - {label: Flatworm mitochondrial, value: '14'}
                - {label: Blepharisma macronuclear, value: '15'}
                - {label: Chlorophycean mitochondrial, value: '16'}
                - {label: Trematode mitochondrial, value: '21'}
                - {label: Scenedesmus obliquus, value: '22'}
                - {label: Thraustochytrium mitochondrial, value: '23'}
    - !mobyle/inputprogramparagraph
        prompt: Output section
        name: output
        children:
        - !mobyle/inputprogramparameter {prompt: Name of the output file (outfile),
            format: '("" , " -outfile=" + str(value))[value is not None]', argpos: 3,
            name: outfile, command: false}
        - !mobyle/inputprogramparameter {prompt: Choose the sequence output format,
            format: '("", " -osformat=" + str(value))[value is not None and value!=vdef]',
            argpos: 4, name: osformat_outfile, command: false}
    - !mobyle/inputprogramparameter
        prompt: Turn off any prompting
        format: '" -auto -stdout"'
        argpos: 5
        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:2977']
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"backtranambig.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"backtranambig.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0371']
topics: ['EDAM_topic:0108']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/backtranambig.html',
    'http://emboss.sourceforge.net/docs/themes']
command: backtranambig
env: {}