fastq_box_plot_0.0.13.yaml

!mobyle/program
name: fastq_box_plot
version: 0.0.13
title: FASTX Toolkit - FASTX Quality Box Plot
description: Generates a solexa quality score box-plot graph.
authors: Assaf Gordon
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparagraph
        prompt: Input
        name: input
        argpos: 1
        children:
        - !mobyle/inputprogramparameter {comment: Input file should be the output
                of "solexa_quality_statistics" program, prompt: FASTX Quality File
                (-i), format: '" -i " + str( value )', simple: true, argpos: 2, mandatory: true,
            name: input_file, command: false}
    - !mobyle/inputprogramparagraph
        prompt: Options
        name: output_para
        children:
        - !mobyle/inputprogramparameter
            comment: Generate PostScript (.PS) file - Default is PNG image
            prompt: Generate PostScript? (-p)
            format: ''' -p'''
            argpos: 3
            name: generate_postscript
            command: false
            hidden: true
            type: !mobyle/booleantype {}
        - !mobyle/inputprogramparameter
            comment: Title (usually the solexa file name) - will be plotted on the
                graph
            prompt: Enter title of the box-plot graph (-t)
            format: ('', ' -t ' + str(value))[value is not None]
            simple: true
            argpos: 4
            name: chart_title
            command: false
            type: !mobyle/stringtype {}
    - !mobyle/inputprogramparagraph
        prompt: Output
        name: Output
        argpos: 6
        children:
        - !mobyle/inputprogramparameter
            comment: Output file name - default is STDOUT
            prompt: Enter output file prefix (-o)
            format: (" -o " + str(vdef) , " -o " + str(value))[value is not None]
                + ".ps"
            simple: true
            argpos: 7
            name: output_file
            command: false
            type: !mobyle/stringtype {default: quality_chart}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparagraph
        prompt: Output
        name: Output
        argpos: 6
        children:
        - !mobyle/outputprogramparameter {prompt: OutSequence, filenames: '"*.ps"',
            name: quality_out}
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"fastq_box_plot.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"fastq_box_plot.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_topic:3218']
topics: ['EDAM_topic:3168', 'EDAM_topic:0092']
command: fastq_quality_boxplot_graph.sh
env: {}