chips.yaml

!mobyle/program
name: chips
title: chips
description: Calculates Nc codon usage statistic
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparagraph
        prompt: Input section
        name: input
        children:
        - !mobyle/inputprogramparameter
            prompt: Seqall option
            format: ("", " -seqall=" + str(value))[value is not None]
            simple: true
            argpos: 1
            mandatory: true
            name: seqall
            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: Advanced section
        name: advanced
        children:
        - !mobyle/inputprogramparameter
            prompt: Sum codons over all sequences
            format: (" -nosum", "")[ bool(value) ]
            argpos: 2
            name: sum
            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: 3
            name: outfile
            command: false
            type: !mobyle/stringtype {default: chips.outfile}
    - !mobyle/inputprogramparameter
        prompt: Turn off any prompting
        format: '" -auto -stdout"'
        argpos: 4
        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: Standard output
        filenames: '"chips.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"chips.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0286']
topics: ['EDAM_topic:0107']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/chips.html', 'http://emboss.sourceforge.net/docs/themes']
command: chips
env: {}