checktrans.yaml

!mobyle/program
name: checktrans
title: checktrans
description: Reports STOP codons and ORF statistics of a protein
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: Required section
        name: required
        children:
        - !mobyle/inputprogramparameter
            prompt: Minimum orf length to report (value greater than or equal to 1)
            format: ("", " -orfml=" + str(value))[value is not None and value!=vdef]
            simple: true
            argpos: 2
            mandatory: true
            name: orfml
            command: false
            type: !mobyle/integertype {default: 100}
            ctrls:
            -   message: Value greater than or equal to 1 is required
                test:
                    value: {'#gte': '1'}
    - !mobyle/inputprogramparagraph
        prompt: Additional section
        name: additional
        children:
        - !mobyle/inputprogramparameter
            comment: An asterisk in the protein sequence indicates the position of
                a STOP codon. Checktrans assumes that all ORFs end in a STOP  codon.
                Forcing the sequence to end with an asterisk, if there is  not one
                there already, makes checktrans treat the end as a  potential ORF.
                If an asterisk is added, it is not included in the  reported count
                of STOPs.
            prompt: Force the sequence to end with an asterisk
            format: (" -noaddlast", "")[ bool(value) ]
            argpos: 3
            name: addlast
            command: false
            type: !mobyle/booleantype {default: false}
    - !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: 4
            name: outfile
            command: false
            type: !mobyle/stringtype {default: checktrans.outfile}
        - !mobyle/inputprogramparameter
            comment: Sequence file to hold output ORF sequences
            prompt: Name of the output sequence file (outseq)
            format: ("" , " -outseq=" + str(value))[value is not None]
            argpos: 5
            name: outseq
            command: false
            type: !mobyle/stringtype {default: checktrans.outseq}
        - !mobyle/inputprogramparameter
            prompt: Choose the sequence output format
            format: ("", " -osformat=" + str(value))[value is not None and value!=vdef]
            argpos: 6
            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 {comment: File for output features, prompt: Name
                of the output feature file (outfeat), format: '("" , " -outfeat="
                + str(value))[value is not None]', argpos: 7, name: outfeat, command: false}
        - !mobyle/inputprogramparameter {prompt: Choose the feature output format,
            format: '("", " -offormat=" + str(value))[value is not None and value!=vdef]',
            argpos: 8, name: offormat_outfeat, command: false}
    - !mobyle/inputprogramparameter
        prompt: Turn off any prompting
        format: '" -auto -stdout"'
        argpos: 9
        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: Outfeat_out option, filenames: outfeat,
            name: outfeat_out}
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"checktrans.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"checktrans.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0436']
topics: ['EDAM_topic:0109']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/checktrans.html', 'http://emboss.sourceforge.net/docs/themes']
command: checktrans
env: {}