codonw_1.4.4.yaml

!mobyle/program
name: codonw
version: 1.4.4
title: codonw
description: Correspondence Analysis of Codon Usage
authors: J. Peden
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter
        format: '"codonw -silent -nomenu -nowarn"'
        argpos: 0
        name: codonw
        command: true
        hidden: true
        type: !mobyle/stringtype {}
    - !mobyle/inputprogramparameter
        format: '" " + str(seqfile) + ".indices " + str(seqfile) + ".bulk"'
        argpos: 2000
        name: outfiles
        command: false
        hidden: true
        type: !mobyle/stringtype {}
    - !mobyle/inputprogramparameter
        prompt: Sequences File
        format: '" " + str(value)'
        simple: true
        argpos: 1000
        mandatory: true
        name: seqfile
        command: false
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:2200']
            data_terms: ['EDAM_data:2044']
    - !mobyle/inputprogramparagraph
        prompt: Defaults settings
        name: defaults
        children:
        - !mobyle/inputprogramparameter
            prompt: Genetic codes (-code)
            format: ( ""  , " -code " + str(value) )[value is not None and value !=
                vdef]
            argpos: 2
            name: gc
            command: false
            type: !mobyle/stringtype
                default: '0'
                options:
                - {label: 'Universal Genetic code [TGA=* TAA=* TAG=*] (0)', value: '0'}
                - {label: 'Vertebrate Mitochondrial code [AGR=* ATA=M TGA=W] (1)',
                    value: '1'}
                - {label: 'Yeast Mitochondrial code [CTN=* ATA=M TGA=W] (2)', value: '2'}
                - {label: 'Filamentous fungi Mitochondrial code [TGA=W] (3)', value: '3'}
                - {label: 'Insects and Plathyhelminthes Mitochondrial co [ATA=M TGA=W
                        AGR=S] (4)', value: '4'}
                - {label: 'Nuclear code of Cilitia [UAA=Q=Gln UAG=Q] (5)', value: '5'}
                - {label: 'Nuclear code of Euplotes [UGA=C] (6)', value: '6'}
                - {label: Mitochondrial code of Echinoderms UGA=W AGR=S AAA=N (7),
                    value: '7'}
        - !mobyle/inputprogramparameter
            prompt: Fop/CBI codons (-f_type)
            format: ( ""  , " -f_type " + str(value) )[ value is not None and value
                != vdef]
            argpos: 2
            name: fop_values
            command: false
            type: !mobyle/stringtype
                default: '0'
                options:
                - {label: Escherichia coli (0), value: '0'}
                - {label: Bacillus subtilis (1), value: '1'}
                - {label: Dictyostelium discoideum (2), value: '2'}
                - {label: Aspergillus nidulans (3), value: '3'}
                - {label: Saccharomyces cerevisiae (4), value: '4'}
                - {label: Drosophila melanogaster (5), value: '5'}
                - {label: Caenorhabditis elegans (6), value: '6'}
                - {label: Neurospora crassa (7), value: '7'}
        - !mobyle/inputprogramparameter
            prompt: CAI fitness values (-c_type)
            format: ( ""  , " -c_type " + str(value) )[value is not None and value
                != vdef]
            argpos: 2
            name: cai_values
            command: false
            type: !mobyle/stringtype
                default: '0'
                options:
                - {label: Escherichia coli (0), value: '0'}
                - {label: Bacillus subtilis (1), value: '1'}
                - {label: Saccharomyces cerevisiae (2), value: '2'}
        - !mobyle/inputprogramparameter
            prompt: Output Computer readable (-machine)
            format: ( ""  , " -machine" )[ value ]
            argpos: 2
            name: output_type
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Concatenate all genes instead of individual genes (-totals)
            format: ( ""  , " -totals" )[ value ]
            argpos: 3
            name: genes
            command: false
            type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparagraph
        prompt: Codon usage indices
        name: CU_options
        argpos: 4
        children:
        - !mobyle/inputprogramparameter
            prompt: All indices (-all_indices)
            format: ( ""  , " -all_indices" )[ value ]
            name: all_indices
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparagraph
            prompt: Special indices
            name: sp_indices
            precond: {'#not': all_indices}
            children:
            - !mobyle/inputprogramparameter
                prompt: Codon Adaptation Index (-cai)
                format: ( ""  , " -cai" )[ value ]
                name: CAI
                command: false
                type: !mobyle/booleantype {default: false}
            - !mobyle/inputprogramparameter {prompt: User input file of CAI values
                    (-cai_file), format: '( ""  , " -cai_file " + str(value) )[value
                    is not None]', argpos: 2, name: cai_file, precond: CAI, command: false}
            - !mobyle/inputprogramparameter
                prompt: Frequency of OPtimal codons index (-fop)
                format: ( ""  , " -fop" )[ value ]
                name: Fop
                command: false
                type: !mobyle/booleantype {default: false}
            - !mobyle/inputprogramparameter {prompt: User input file of Fop values
                    (-fop_file), format: '( ""  , " -fop_file " + str(value) )[ value
                    is not None ]', argpos: 2, name: fop_file, precond: Fop, command: false}
            - !mobyle/inputprogramparameter
                prompt: Codon bias index (-cbi)
                format: ( ""  , " -cbi" )[ value ]
                name: CBI
                command: false
                type: !mobyle/booleantype {default: false}
            - !mobyle/inputprogramparameter {prompt: User input file of CBI values
                    (-cbi_file), format: '( ""  , " -cbi_file " + str(value) )[ value
                    is not None ]', argpos: 2, name: cbi_file, precond: CBI, command: false}
            - !mobyle/inputprogramparameter
                prompt: Effective Number of Codons (-enc)
                format: ( ""  , " -enc" )[ value ]
                name: ENc
                command: false
                type: !mobyle/booleantype {default: false}
            - !mobyle/inputprogramparameter
                prompt: GC content of gene (-gc)
                format: ( ""  , " -gc" )[ value ]
                name: GC
                command: false
                type: !mobyle/booleantype {default: false}
            - !mobyle/inputprogramparameter
                prompt: GC of silent 3rd codon posit. (-gc3s)
                format: ( ""  , " -gc3s" )[ value ]
                name: GC3s
                command: false
                type: !mobyle/booleantype {default: false}
            - !mobyle/inputprogramparameter
                prompt: Base composition at synonymous third codon positions (-sil_base)
                format: ( ""  , " -sil_base" )[ value ]
                name: silent_bc
                command: false
                type: !mobyle/booleantype {default: false}
            - !mobyle/inputprogramparameter
                prompt: Number of synonymous codons (-L_sym)
                format: ( "" , " -L_sym" )[ value ]
                name: L_sym
                command: false
                type: !mobyle/booleantype {default: false}
            - !mobyle/inputprogramparameter
                prompt: Total Number of synonymous and non-synonymous codons (-L_aa)
                format: ( ""  , " -L_aa" )[ value ]
                name: L_aa
                command: false
                type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparagraph
        prompt: Amino acid indices
        name: AA_options
        children:
        - !mobyle/inputprogramparameter
            prompt: Hydrophobicity of protein (-hyd)
            format: ( ""  , " -hyd" )[ value ]
            argpos: 4
            name: Hydro
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Aromaticity of protein (-aro)
            format: ( ""  , " -aro" )[ value ]
            argpos: 4
            name: Aromo
            command: false
            type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparameter
        prompt: Bulk output option
        format: ( ""  , " " + str(value) )[ value is not None and value != vdef]
        argpos: 4
        name: bulk_output_option
        command: false
        type: !mobyle/stringtype
            default: -cu
            options:
            - {label: Codon Usage (-cu), value: -cu}
            - {label: Amino Acid Usage (-aau), value: -aau}
            - {label: Relative Amino Acid Usage (-raau), value: -raau}
            - {label: Tabulation of codon usage (-cutab), value: -cutab}
            - {label: Tabulation of dataset's codon usage (-cutot), value: -cutot}
            - {label: Relative Synonymous Codon Usage (-rscu), value: -rscu}
            - {label: Fasta format (-fasta), value: -fasta}
            - {label: Reader format with codons are seperated by spaces (-reader),
                value: -reader}
            - {label: Conceptual translation of DNA to amino acid (-transl), value: -transl}
            - {label: Detailed report of codon G+C composition (-base), value: -base}
            - {label: Dinucleotide usage of the three codon position (-dinuc), value: -dinuc}
            - {label: No bulk output to be written to file (-noblk), value: -noblk}
    - !mobyle/inputprogramparameter
        prompt: Correspondence analysis options (available for several sequences)
        format: ( "" , " %s" %value)[value is not None]
        argpos: 3
        name: COA_option
        command: false
        type: !mobyle/stringtype
            default: 'Null'
            options:
            - {label: Do not perform a COA, value: 'Null'}
            - {label: COA of codon usage frequencies (-coa_cu), value: -coa_cu}
            - {label: COA of Relative Synonymous Codon Usage (-coa_rscu), value: -coa_rscu}
            - {label: COA on Amino Acid usage frequencies (-coa_aa), value: -coa_aa}
    - !mobyle/inputprogramparagraph
        prompt: Advanced COA options
        name: coa_advanced
        precond: COA_option
        children:
        - !mobyle/inputprogramparameter
            prompt: Generate detailed (expert) statistics on COA (-coa_expert)
            format: ( ""  , " -coa_expert" )[ value ]
            argpos: 3
            name: coa_expert
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Select number of axis to record (-coa_axes)
            format: (  "" , "  -coa_axes " +  str(value) )[value is not None and value!=vdef]
            argpos: 3
            name: coa_axes
            command: false
            type: !mobyle/integertype {default: 4}
        - !mobyle/inputprogramparameter
            comment: Values can be whole numbers or a percentage (5 or 10%).
            prompt: Select number of genes to use to identify optimal codons (-coa_num)
            format: ( ""  , " -coa_num " + str(value) )[ value is not None ]
            argpos: 3
            name: coa_num
            command: false
            type: !mobyle/integertype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter {prompt: Results files, filenames: '"*.bulk"',
        name: results_files}
    - !mobyle/outputprogramparagraph
        prompt: Advanced COA options
        name: coa_advanced
        precond: COA_option
        children:
        - !mobyle/outputprogramparameter {prompt: Coa file, filenames: '"coa_raw"',
            name: coa_files}
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"codonw.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"codonw.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
documentation_links: ['http://codonw.sourceforge.net/Readme.html', 'http://codonw.sourceforge.net/Tutorial.html']
homepage_links: ['http://codonw.sourceforge.net/']
env: {}
source_links: ['http://sourceforge.net/projects/codonw/files/']