mobyle2.services/blast2taxonomy_2.0.yaml at master · mobyle2/mobyle2.services · GitHub

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!mobyle/program
name: blast2taxonomy
version: '2.0'
title: blast2taxonomy
description: Blast Taxonomy report
authors: C. Maufrais
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter
        prompt: Blast output file
        format: '" " + str(value)'
        simple: true
        argpos: 10
        mandatory: true
        name: infile
        command: false
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:0857']
    - !mobyle/inputprogramparagraph
        prompt: Display options
        name: display
        argpos: 1
        children:
        - !mobyle/inputprogramparameter
            comment: All hit are display in tree by default.
            prompt: Report one branch per organism (-s)
            format: ("" , " -s") [value]
            name: single
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Report accession number (-a)
            format: ("" , " -a") [value]
            name: acc
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Lowest common ancestor name (-n).
            format: ("" , " -n " + str(value)) [value is not None]
            name: node_name
            command: false
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            prompt: Select hit blast with e-value lower than value (-E).
            format: ("" , " -E " + str(value)) [value and value != vdef]
            name: filterevalue
            command: false
            type: !mobyle/floattype {default: 10.0}
        - !mobyle/inputprogramparameter
            prompt: Report score and e-value Blast hit (-e).
            format: ("" , " -e") [value]
            name: evalue
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Report ratio of Blast hit length per query length (-l).
            format: ("" , " -l") [value]
            name: perlen
            command: false
            type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparagraph
        prompt: Output option
        name: output
        children:
        - !mobyle/inputprogramparameter
            prompt: Tabular output (-x)
            format: ("" , " -x") [value]
            name: xlsoutput
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Html output (-w)
            format: ("" , " -w") [value]
            name: htmloutput
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Taxonomy report in Newick format (-t)
            format: ("" , " -t") [value]
            name: dndoutput
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Output file name (-o)
            format: (""  , " -o  " + str(value))  [value is not None ]
            name: outputfile
            command: false
            type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparagraph
        prompt: Output option
        name: output
        children:
        - !mobyle/outputprogramparameter
            prompt: Output file
            filenames: str(outputfile)
            name: outfile_name
            precond:
                '#and':
                - {'#not': htmloutput}
                - outputfile
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2048']
        - !mobyle/outputprogramparameter
            prompt: Output file
            filenames: '"blast2taxonomy.out"'
            name: outfile
            precond:
                '#not':
                    '#and': [htmloutput, outputfile]
            output_type: stdout
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2048']
        - !mobyle/outputprogramparameter
            prompt: Html output file
            filenames: ("blast2taxonomy.html", str(outputfile)+".html")[outputfile
                is not None]
            name: htmloutfile
            precond: htmloutput
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2048']
        - !mobyle/outputprogramparameter
            prompt: Alignment Html output file
            filenames: '"alignment.html"'
            name: htmloutfilealn
            precond: htmloutput
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2048']
        - !mobyle/outputprogramparameter
            prompt: Newick tree file
            filenames: ("blast2taxonomy.dnd", str(outputfile)+".dnd")[outputfile is
                not None]
            name: dndoutfile
            precond: dndoutput
            type: !mobyle/formattedtype
                format_terms: ['EDAM_format:1910']
                data_terms: ['EDAM_data:0872']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"blast2taxonomy.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0258', 'EDAM_operation:0637']
topics: ['EDAM_topic:0182', 'EDAM_topic:0637']
command: blast2taxonomy
env: {}