density.yaml

!mobyle/program
name: density
title: density
description: Draw a nucleic acid density 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:2977']
    - !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: 2
            name: window
            command: false
            type: !mobyle/integertype {default: 100}
            ctrls:
            -   message: Value greater than or equal to 1 is required
                test:
                    value: {'#gte': '1'}
        - !mobyle/inputprogramparameter
            prompt: Graph type
            format: ("", " -display=" + str(value))[value is not None and value!=vdef]
            argpos: 3
            name: display
            command: false
            type: !mobyle/stringtype
                default: none
                options:
                - {label: Dual - graphic showing individual bases, value: D}
                - {label: Quad - at vs gc graphic, value: Q}
                - {label: None, value: none}
    - !mobyle/inputprogramparagraph
        prompt: Output section
        name: output
        children:
        - !mobyle/inputprogramparameter
            prompt: Choose the graph output format
            format: (" -graph=" + str(vdef), " -graph=" + str(value))[value is not
                None and value!=vdef]
            argpos: 4
            name: graph
            precond:
                display: {'#ne': none}
            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: 5
            name: xy_goutfile
            precond:
                display: {'#ne': none}
            command: false
            type: !mobyle/stringtype {default: density_xygraph}
        - !mobyle/inputprogramparameter
            prompt: Name of the report file
            format: ("" , " -outfile=" + str(value))[value is not None]
            argpos: 6
            name: outfile
            precond: {display: none}
            command: false
            type: !mobyle/stringtype {default: density.report}
        - !mobyle/inputprogramparameter
            prompt: Choose the report output format
            format: ("", " -rformat=" + str(value))[value is not None and value!=vdef]
            argpos: 7
            name: rformat_outfile
            precond: {display: none}
            command: false
            type: !mobyle/stringtype
                default: TABLE
                options:
                - {label: Dasgff, value: DASGFF}
                - {label: Dbmotif, value: DBMOTIF}
                - {label: Diffseq, value: DIFFSEQ}
                - {label: Embl, value: EMBL}
                - {label: Excel, value: EXCEL}
                - {label: Feattable, value: FEATTABLE}
                - {label: Genbank, value: GENBANK}
                - {label: Gff, value: GFF}
                - {label: Listfile, value: LISTFILE}
                - {label: Motif, value: MOTIF}
                - {label: Nametable, value: NAMETABLE}
                - {label: Pir, value: PIR}
                - {label: Regions, value: REGIONS}
                - {label: Seqtable, value: SEQTABLE}
                - {label: Simple, value: SIMPLE}
                - {label: Srs, value: SRS}
                - {label: Swiss, value: SWISS}
                - {label: Table, value: TABLE}
                - {label: Tagseq, value: TAGSEQ}
    - !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':
                -   display: {'#ne': none}
                - {graph: png}
        - !mobyle/outputprogramparameter
            prompt: Graph file
            filenames: '"*.gif"'
            name: xy_outgraph_gif
            precond:
                '#and':
                -   display: {'#ne': none}
                - {graph: gif}
        - !mobyle/outputprogramparameter
            prompt: Graph file
            filenames: '"*.ps"'
            name: xy_outgraph_ps
            precond:
                '#or':
                -   '#and':
                    -   display: {'#ne': none}
                    - {graph: ps}
                - {graph: cps}
        - !mobyle/outputprogramparameter
            prompt: Graph file
            filenames: '"*.meta"'
            name: xy_outgraph_meta
            precond:
                '#and':
                -   display: {'#ne': none}
                - {graph: meta}
        - !mobyle/outputprogramparameter
            prompt: Graph file
            filenames: '"*.dat"'
            name: xy_outgraph_data
            precond:
                '#and':
                -   display: {'#ne': none}
                - {graph: data}
        - !mobyle/outputprogramparameter
            prompt: Outfile_out option
            filenames: outfile
            name: outfile_out
            precond:
                rformat_outfile:
                    '#in': [DASGFF, DBMOTIF, DIFFSEQ, EMBL, EXCEL, FEATTABLE, GENBANK,
                        GFF, LISTFILE, MOTIF, NAMETABLE, PIR, REGIONS, SEQTABLE, SIMPLE,
                        SRS, SWISS, TABLE, TAGSEQ]
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"density.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"density.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0377']
topics: ['EDAM_topic:0157']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/density.html', 'http://emboss.sourceforge.net/docs/themes']
command: density
env: {}