einverted.yaml

!mobyle/program
name: einverted
title: einverted
description: Finds inverted repeats in nucleotide sequences
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
            prompt: Gap penalty
            format: ("", " -gap=" + str(value))[value is not None and value!=vdef]
            simple: true
            argpos: 2
            mandatory: true
            name: gap
            command: false
            type: !mobyle/integertype {default: 12}
        - !mobyle/inputprogramparameter
            prompt: Minimum score threshold
            format: ("", " -threshold=" + str(value))[value is not None and value!=vdef]
            simple: true
            argpos: 3
            mandatory: true
            name: threshold
            command: false
            type: !mobyle/integertype {default: 50}
        - !mobyle/inputprogramparameter
            prompt: Match score
            format: ("", " -match=" + str(value))[value is not None and value!=vdef]
            simple: true
            argpos: 4
            mandatory: true
            name: match
            command: false
            type: !mobyle/integertype {default: 3}
        - !mobyle/inputprogramparameter
            prompt: Mismatch score
            format: ("", " -mismatch=" + str(value))[value is not None and value!=vdef]
            simple: true
            argpos: 5
            mandatory: true
            name: mismatch
            command: false
            type: !mobyle/integertype {default: -4}
    - !mobyle/inputprogramparagraph
        prompt: Additional section
        name: additional
        children:
        - !mobyle/inputprogramparameter
            comment: Maximum separation between the start of repeat and the end of
                the inverted repeat (the default is 2000 bases).
            prompt: Maximum extent of repeats
            format: ("", " -maxrepeat=" + str(value))[value is not None and value!=vdef]
            argpos: 6
            name: maxrepeat
            command: false
            type: !mobyle/integertype {default: 2000}
    - !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: 7
            name: outfile
            command: false
            type: !mobyle/stringtype {default: outfile.inv}
        - !mobyle/inputprogramparameter
            comment: The sequence of the inverted repeat regions without gap characters.
            prompt: Name of the output sequence file (outseq)
            format: ("" , " -outseq=" + str(value))[value is not None]
            argpos: 8
            name: outseq
            command: false
            type: !mobyle/stringtype {default: einverted.outseq}
        - !mobyle/inputprogramparameter
            prompt: Choose the sequence output format
            format: ("", " -osformat=" + str(value))[value is not None and value!=vdef]
            argpos: 9
            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: 10
        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: Outseq_out option
            filenames: outseq
            name: outseq_out
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"einverted.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"einverted.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0379', 'EDAM_operation:0278']
topics: ['EDAM_topic:0157']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/einverted.html', 'http://emboss.sourceforge.net/docs/themes']
command: einverted
env: {}