dotpath.yaml

!mobyle/program
name: dotpath
title: dotpath
description: Draw a non-overlapping wordmatch dotplot of two sequences
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparagraph
        prompt: Input section
        name: input
        children:
        - !mobyle/inputprogramparameter
            prompt: Asequence option
            format: ("", " -asequence=" + str(value))[value is not None]
            simple: true
            argpos: 1
            mandatory: true
            name: asequence
            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:2044']
        - !mobyle/inputprogramparameter
            prompt: Bsequence option
            format: ("", " -bsequence=" + str(value))[value is not None]
            simple: true
            argpos: 2
            mandatory: true
            name: bsequence
            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:2044']
    - !mobyle/inputprogramparagraph
        prompt: Required section
        name: required
        children:
        - !mobyle/inputprogramparameter
            prompt: Word size (value greater than or equal to 2)
            format: ("", " -wordsize=" + str(value))[value is not None and value!=vdef]
            simple: true
            argpos: 3
            mandatory: true
            name: wordsize
            command: false
            type: !mobyle/integertype {default: 4}
            ctrls:
            -   message: Value greater than or equal to 2 is required
                test:
                    value: {'#gte': '2'}
    - !mobyle/inputprogramparagraph
        prompt: Output section
        name: output
        children:
        - !mobyle/inputprogramparameter
            comment: Displays the overlapping matches (in red) as well as the minimal
                set of non-overlapping matches
            prompt: Display the overlapping matches
            format: ("", " -overlaps")[ bool(value) ]
            argpos: 4
            name: overlaps
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Draw a box around dotplot
            format: (" -noboxit", "")[ bool(value) ]
            argpos: 5
            name: boxit
            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]
            simple: true
            argpos: 6
            mandatory: true
            name: graph
            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: 7
            name: goutfile
            command: false
            type: !mobyle/stringtype {default: dotpath_graph}
    - !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: outgraph_png
            precond: {graph: png}
        - !mobyle/outputprogramparameter
            prompt: Graph file
            filenames: '"*.gif"'
            name: outgraph_gif
            precond: {graph: gif}
        - !mobyle/outputprogramparameter
            prompt: Graph file
            filenames: '"*.ps"'
            name: outgraph_ps
            precond:
                '#or':
                - {graph: ps}
                - {graph: cps}
        - !mobyle/outputprogramparameter
            prompt: Graph file
            filenames: '"*.meta"'
            name: outgraph_meta
            precond: {graph: meta}
        - !mobyle/outputprogramparameter
            prompt: Graph file
            filenames: '"*.dat"'
            name: outgraph_data
            precond: {graph: data}
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"dotpath.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"dotpath.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0288', 'EDAM_operation:0490']
topics: ['EDAM_topic:0159']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/dotpath.html', 'http://emboss.sourceforge.net/docs/themes']
command: dotpath
env: {}