charge.yaml

!mobyle/program
name: charge
title: charge
description: Draw a protein charge plot
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:2976']
        - !mobyle/inputprogramparameter {prompt: Amino acids properties and molecular
                weight data file, format: '("", " -aadata=" + str(value))[value is
                not None ]', argpos: 2, name: aadata, command: false}
    - !mobyle/inputprogramparagraph
        prompt: Additional section
        name: additional
        children:
        - !mobyle/inputprogramparameter
            prompt: Window length (value greater than or equal to 1)
            format: ("", " -window=" + str(value))[value is not None and value!=vdef]
            argpos: 3
            name: window
            command: false
            type: !mobyle/integertype {default: 5}
            ctrls:
            -   message: Value greater than or equal to 1 is required
                test:
                    value: {'#gte': '1'}
    - !mobyle/inputprogramparagraph
        prompt: Output section
        name: output
        children:
        - !mobyle/inputprogramparameter
            prompt: Produce graphic
            format: ("", " -plot")[ bool(value) ]
            argpos: 4
            name: plot
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Choose the graph output format
            format: (" -graph=" + str(vdef), " -graph=" + str(value))[value is not
                None and value!=vdef]
            argpos: 5
            name: graph
            precond: plot
            command: false
            type: !mobyle/stringtype
                default: png
                options:
                - {label: Png, value: png}
                - {label: Gif, value: gif}
                - {label: Cps, value: cps}
                - {label: Ps, value: ps}
                - {label: Meta, value: meta}
                - {label: Data, value: data}
        - !mobyle/inputprogramparameter
            prompt: Name of the output graph
            format: ("" , " -goutfile=" + str(value))[value is not None]
            argpos: 6
            name: xy_goutfile
            precond: plot
            command: false
            type: !mobyle/stringtype {default: charge_xygraph}
        - !mobyle/inputprogramparameter
            prompt: Name of the output file (outfile)
            format: ("" , " -outfile=" + str(value))[value is not None]
            argpos: 7
            name: outfile
            precond: {'#not': plot}
            command: false
            type: !mobyle/stringtype {default: charge.outfile}
    - !mobyle/inputprogramparameter
        prompt: Turn off any prompting
        format: '" -auto -stdout"'
        argpos: 8
        name: auto
        command: false
        hidden: true
        type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparagraph
        prompt: Output section
        name: output
        children:
        - !mobyle/outputprogramparameter
            prompt: Graph file
            filenames: '"*.png"'
            name: xy_outgraph_png
            precond:
                '#and':
                - plot
                - {graph: png}
        - !mobyle/outputprogramparameter
            prompt: Graph file
            filenames: '"*.gif"'
            name: xy_outgraph_gif
            precond:
                '#and':
                - plot
                - {graph: gif}
        - !mobyle/outputprogramparameter
            prompt: Graph file
            filenames: '"*.ps"'
            name: xy_outgraph_ps
            precond:
                '#or':
                -   '#and':
                    - plot
                    - {graph: ps}
                - {graph: cps}
        - !mobyle/outputprogramparameter
            prompt: Graph file
            filenames: '"*.meta"'
            name: xy_outgraph_meta
            precond:
                '#and':
                - plot
                - {graph: meta}
        - !mobyle/outputprogramparameter
            prompt: Graph file
            filenames: '"*.dat"'
            name: xy_outgraph_data
            precond:
                '#and':
                - plot
                - {graph: data}
        - !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: '"charge.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"charge.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0405']
topics: ['EDAM_topic:0137']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/charge.html', 'http://emboss.sourceforge.net/docs/themes']
command: charge
env: {}