extractalign.yaml

!mobyle/program
name: extractalign
title: extractalign
description: Extract regions from a sequence alignment
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:2200', 'EDAM_format:1993', 'EDAM_format:1996',
                    'EDAM_format:1985', 'EDAM_format:1986', 'EDAM_format:1988', 'EDAM_format:1989',
                    'EDAM_format:1987', 'EDAM_format:2002', 'EDAM_format:2003', 'EDAM_format:1999',
                    'EDAM_format:2001', 'EDAM_format:2001', 'EDAM_format:2001', 'EDAM_format:1990']
                data_terms: ['EDAM_data:0863']
    - !mobyle/inputprogramparagraph
        prompt: Required section
        name: required
        children:
        - !mobyle/inputprogramparameter
            comment: "Regions to extract. \n A set of regions is specified by a set\
                \ of pairs of positions. \n  The positions are integers. \n  They\
                \ are separated by any non-digit, non-alpha character. \n  Examples\
                \ of region specifications are: \n  24-45, 56-78 \n  1:45, 67=99;765..888\
                \ \n  1,5,8,10,23,45,57,99"
            prompt: 'Regions to extract (eg: 4-57,78-94)'
            format: ("", " -regions=" + str(value))[value is not None]
            simple: true
            argpos: 2
            mandatory: true
            name: regions
            command: false
            type: !mobyle/stringtype {}
    - !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: 3
            name: outseq
            command: false
            type: !mobyle/stringtype {default: extractalign.outseq}
        - !mobyle/inputprogramparameter
            prompt: Choose the sequence output format
            format: ("", " -osformat=" + str(value))[value is not None and value!=vdef]
            argpos: 4
            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: 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: Outseq_out option
            filenames: outseq
            name: outseq_out
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"extractalign.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"extractalign.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:2122']
topics: ['EDAM_topic:0187']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/extractalign.html', 'http://emboss.sourceforge.net/docs/themes']
command: extractalign
env: {}