cirdna.yaml

!mobyle/program
name: cirdna
title: cirdna
description: Draws circular maps of DNA constructs
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparagraph
        prompt: Input section
        name: input
        children:
        - !mobyle/inputprogramparameter {prompt: Commands to the cirdna drawing program
                file, format: '("", " -infile=" + str(value))[value is not None ]',
            simple: true, argpos: 1, mandatory: true, name: infile, command: false}
    - !mobyle/inputprogramparagraph
        prompt: Additional section
        name: additional
        children:
        - !mobyle/inputprogramparameter
            prompt: Maximum number of groups (value greater than or equal to 1)
            format: ("", " -maxgroups=" + str(value))[value is not None and value!=vdef]
            argpos: 2
            name: maxgroups
            command: false
            type: !mobyle/integertype {default: 20}
            ctrls:
            -   message: Value greater than or equal to 1 is required
                test:
                    value: {'#gte': '1'}
        - !mobyle/inputprogramparameter
            prompt: Maximum number of labels (value greater than or equal to 1)
            format: ("", " -maxlabels=" + str(value))[value is not None and value!=vdef]
            argpos: 3
            name: maxlabels
            command: false
            type: !mobyle/integertype {default: 10000}
            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: Draw a ruler
            format: (" -noruler", "")[ bool(value) ]
            argpos: 4
            name: ruler
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Type of blocks
            format: ("", " -blocktype=" + str(value))[value is not None and value!=vdef]
            simple: true
            argpos: 5
            mandatory: true
            name: blocktype
            command: false
            type: !mobyle/stringtype
                default: Filled
                options:
                - {label: Open blocks, value: Open}
                - {label: Filled blocks, value: Filled}
                - {label: Black border, value: Outline}
        - !mobyle/inputprogramparameter
            prompt: Position in degrees of the molecule's origin on the circle (value
                from 0 to 360)
            format: ("", " -originangle=" + str(value))[value is not None and value!=vdef]
            argpos: 6
            name: originangle
            command: false
            type: !mobyle/floattype {default: 90.0}
            ctrls:
            -   message: Value greater than or equal to 0 is required
                test:
                    value: {'#gte': '0'}
            -   message: Value less than or equal to 360 is required
                test:
                    value: {'#lte': '360'}
        - !mobyle/inputprogramparameter
            prompt: Ticks inside or outside the circle
            format: ("", " -posticks=" + str(value))[value is not None and value!=vdef]
            simple: true
            argpos: 7
            mandatory: true
            name: posticks
            command: false
            type: !mobyle/stringtype
                default: '2'
                options:
                - {label: In, value: '1'}
                - {label: Out, value: '2'}
        - !mobyle/inputprogramparameter
            prompt: Text inside or outside the blocks
            format: ("", " -posblocks=" + str(value))[value is not None and value!=vdef]
            simple: true
            argpos: 8
            mandatory: true
            name: posblocks
            command: false
            type: !mobyle/stringtype
                default: '1'
                options:
                - {label: In, value: '1'}
                - {label: Out, value: '2'}
        - !mobyle/inputprogramparameter
            prompt: Horizontal junctions between blocks
            format: (" -nointersymbol", "")[ bool(value) ]
            argpos: 9
            name: intersymbol
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Colour of junctions between blocks (enter a colour number) (value
                from 0 to 15)
            format: ("", " -intercolour=" + str(value))[value is not None and value!=vdef]
            argpos: 10
            name: intercolour
            command: false
            type: !mobyle/integertype {default: 1}
            ctrls:
            -   message: Value greater than or equal to 0 is required
                test:
                    value: {'#gte': '0'}
            -   message: Value less than or equal to 15 is required
                test:
                    value: {'#lte': '15'}
        - !mobyle/inputprogramparameter
            prompt: Horizontal junctions between ticks
            format: ("", " -interticks")[ bool(value) ]
            argpos: 11
            name: interticks
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Interval between ticks in the ruler (value greater than or equal
                to 0)
            format: ("", " -gapsize=" + str(value))[value is not None and value!=vdef]
            argpos: 12
            name: gapsize
            command: false
            type: !mobyle/integertype {default: 500}
            ctrls:
            -   message: Value greater than or equal to 0 is required
                test:
                    value: {'#gte': '0'}
        - !mobyle/inputprogramparameter
            prompt: Vertical lines at the ruler's ticks
            format: ("", " -ticklines")[ bool(value) ]
            argpos: 13
            name: ticklines
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: Height of text. Enter a number <1.0 or >1.0 to decrease or increase
                the size, respectively
            prompt: Text scale factor (value greater than or equal to 0.0)
            format: ("", " -textheight=" + str(value))[value is not None and value!=vdef]
            argpos: 14
            name: textheight
            command: false
            type: !mobyle/floattype {default: 1.0}
            ctrls:
            -   message: Value greater than or equal to 0.0 is required
                test:
                    value: {'#gte': '0.0'}
        - !mobyle/inputprogramparameter
            comment: Length of text. Enter a number <1.0 or >1.0 to decrease or increase
                the size, respectively
            prompt: Length of text multiplier (value greater than or equal to 0.0)
            format: ("", " -textlength=" + str(value))[value is not None and value!=vdef]
            argpos: 15
            name: textlength
            command: false
            type: !mobyle/floattype {default: 1.0}
            ctrls:
            -   message: Value greater than or equal to 0.0 is required
                test:
                    value: {'#gte': '0.0'}
        - !mobyle/inputprogramparameter
            comment: Height of ticks. Enter a number <1.0 or >1.0 to decrease or increase
                the size, respectively
            prompt: Height of ticks multiplier (value greater than or equal to 0.0)
            format: ("", " -tickheight=" + str(value))[value is not None and value!=vdef]
            argpos: 16
            name: tickheight
            command: false
            type: !mobyle/floattype {default: 1.0}
            ctrls:
            -   message: Value greater than or equal to 0.0 is required
                test:
                    value: {'#gte': '0.0'}
        - !mobyle/inputprogramparameter
            comment: Height of blocks. Enter a number <1.0 or >1.0 to decrease or
                increase the size, respectively
            prompt: Height of blocks multiplier (value greater than or equal to 0.0)
            format: ("", " -blockheight=" + str(value))[value is not None and value!=vdef]
            argpos: 17
            name: blockheight
            command: false
            type: !mobyle/floattype {default: 1.0}
            ctrls:
            -   message: Value greater than or equal to 0.0 is required
                test:
                    value: {'#gte': '0.0'}
        - !mobyle/inputprogramparameter
            comment: Height of range ends. Enter a number <1.0 or >1.0 to decrease
                or increase the size, respectively
            prompt: Height of range ends multiplier (value greater than or equal to
                0.0)
            format: ("", " -rangeheight=" + str(value))[value is not None and value!=vdef]
            argpos: 18
            name: rangeheight
            command: false
            type: !mobyle/floattype {default: 1.0}
            ctrls:
            -   message: Value greater than or equal to 0.0 is required
                test:
                    value: {'#gte': '0.0'}
        - !mobyle/inputprogramparameter
            comment: Space between groups. Enter a number <1.0 or >1.0 to decrease
                or increase the size, respectively
            prompt: Space between groups multiplier (value greater than or equal to
                0.0)
            format: ("", " -gapgroup=" + str(value))[value is not None and value!=vdef]
            argpos: 19
            name: gapgroup
            command: false
            type: !mobyle/floattype {default: 1.0}
            ctrls:
            -   message: Value greater than or equal to 0.0 is required
                test:
                    value: {'#gte': '0.0'}
        - !mobyle/inputprogramparameter
            comment: Space between text and ticks, blocks, and ranges. Enter a number
                <1.0 or >1.0 to decrease or increase the size,  respectively
            prompt: Space between text and ticks, blocks, and ranges multiplier (value
                greater than or equal to 0.0)
            format: ("", " -postext=" + str(value))[value is not None and value!=vdef]
            argpos: 20
            name: postext
            command: false
            type: !mobyle/floattype {default: 1.0}
            ctrls:
            -   message: Value greater than or equal to 0.0 is required
                test:
                    value: {'#gte': '0.0'}
        - !mobyle/inputprogramparameter
            prompt: Choose the graphout output format
            format: (" -graphout=" + str(vdef), " -graphout=" + str(value))[value
                is not None and value!=vdef]
            simple: true
            argpos: 21
            mandatory: true
            name: graphout
            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: 22
            name: goutfile
            command: false
            type: !mobyle/stringtype {default: cirdna_graph}
    - !mobyle/inputprogramparameter
        prompt: Turn off any prompting
        format: '" -auto -stdout"'
        argpos: 23
        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: outgraph_png
            precond: {graphout: png}
        - !mobyle/outputprogramparameter
            prompt: Graph file
            filenames: '"*.gif"'
            name: outgraph_gif
            precond: {graphout: gif}
        - !mobyle/outputprogramparameter
            prompt: Graph file
            filenames: '"*.ps"'
            name: outgraph_ps
            precond:
                '#or':
                - {graphout: ps}
                - {graphout: cps}
        - !mobyle/outputprogramparameter
            prompt: Graph file
            filenames: '"*.meta"'
            name: outgraph_meta
            precond: {graphout: meta}
        - !mobyle/outputprogramparameter
            prompt: Graph file
            filenames: '"*.dat"'
            name: outgraph_data
            precond: {graphout: data}
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"cirdna.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"cirdna.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0578']
topics: ['EDAM_topic:0092', 'EDAM_topic:0096']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/cirdna.html', 'http://emboss.sourceforge.net/docs/themes']
command: cirdna
env: {}