etandem.yaml

!mobyle/program
name: etandem
title: etandem
description: Finds tandem repeats in a 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:2977']
    - !mobyle/inputprogramparagraph
        prompt: Required section
        name: required
        children:
        - !mobyle/inputprogramparameter
            prompt: Minimum repeat size (Integer, 2 or higher)
            format: ("", " -minrepeat=" + str(value))[value is not None and value!=vdef]
            simple: true
            argpos: 2
            mandatory: true
            name: minrepeat
            command: false
            type: !mobyle/integertype {default: 10}
            ctrls:
            -   message: Value greater than or equal to 2 is required
                test:
                    value: {'#gte': '2'}
        - !mobyle/inputprogramparameter
            comment: Same as -minrepeat
            prompt: Maximum repeat size (Integer, same as -minrepeat or higher)
            format: ("", " -maxrepeat=" + str(value))[value is not None]
            simple: true
            argpos: 3
            mandatory: true
            name: maxrepeat
            precond: minrepeat
            command: false
            type: !mobyle/integertype {}
    - !mobyle/inputprogramparagraph
        prompt: Advanced section
        name: advanced
        children:
        - !mobyle/inputprogramparameter
            prompt: Threshold score
            format: ("", " -threshold=" + str(value))[value is not None and value!=vdef]
            argpos: 4
            name: threshold
            command: false
            type: !mobyle/integertype {default: 20}
        - !mobyle/inputprogramparameter
            prompt: Allow n as a mismatch
            format: ("", " -mismatch")[ bool(value) ]
            argpos: 5
            name: mismatch
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Allow uniform consensus
            format: ("", " -uniform")[ bool(value) ]
            argpos: 6
            name: uniform
            command: false
            type: !mobyle/booleantype {default: false}
    - !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: 7
            name: outfile
            command: false
            type: !mobyle/stringtype {default: report.tan}
        - !mobyle/inputprogramparameter
            prompt: Choose the report output format
            format: ("", " -rformat=" + str(value))[value is not None and value!=vdef]
            argpos: 8
            name: rformat_outfile
            command: false
            type: !mobyle/stringtype
                default: TABLE
                options:
                - {label: Dasgff, value: DASGFF}
                - {label: Dbmotif, value: DBMOTIF}
                - {label: Diffseq, value: DIFFSEQ}
                - {label: Embl, value: EMBL}
                - {label: Excel, value: EXCEL}
                - {label: Feattable, value: FEATTABLE}
                - {label: Genbank, value: GENBANK}
                - {label: Gff, value: GFF}
                - {label: Listfile, value: LISTFILE}
                - {label: Motif, value: MOTIF}
                - {label: Nametable, value: NAMETABLE}
                - {label: Pir, value: PIR}
                - {label: Regions, value: REGIONS}
                - {label: Seqtable, value: SEQTABLE}
                - {label: Simple, value: SIMPLE}
                - {label: Srs, value: SRS}
                - {label: Swiss, value: SWISS}
                - {label: Table, value: TABLE}
                - {label: Tagseq, value: TAGSEQ}
        - !mobyle/inputprogramparameter
            prompt: Name of the output file (origfile)
            format: ("" , " -origfile=" + str(value))[value is not None]
            argpos: 9
            name: origfile
            command: false
            type: !mobyle/stringtype {default: outfile.oldtan}
    - !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
            precond:
                rformat_outfile:
                    '#in': [DASGFF, DBMOTIF, DIFFSEQ, EMBL, EXCEL, FEATTABLE, GENBANK,
                        GFF, LISTFILE, MOTIF, NAMETABLE, PIR, REGIONS, SEQTABLE, SIMPLE,
                        SRS, SWISS, TABLE, TAGSEQ]
        - !mobyle/outputprogramparameter
            prompt: Origfile_out option
            filenames: origfile
            name: origfile_out
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"etandem.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"etandem.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0379']
topics: ['EDAM_topic:0157']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/etandem.html', 'http://emboss.sourceforge.net/docs/themes']
command: etandem
env: {}