elp_0.0.yaml

!mobyle/program
name: elp
version: '0.0'
title: ELP
description: Evolutionary Landscape Painter
authors: Guillaume Cambray
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter
        prompt: Sequence
        format: ("", " " + str(value))[value is not None]
        simple: true
        argpos: 99
        mandatory: true
        name: sequence
        command: false
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:2200']
            data_terms: ['EDAM_data:2977']
    - !mobyle/inputprogramparameter
        prompt: Number of synonymous sequences to generate (1 to 3)
        format: ( "" , " -n " + str(value) + " ")[value is not None and value != vdef
            ]
        name: sequence_number
        command: false
        type: !mobyle/integertype {default: 1}
        ctrls:
        -   message: minimum is 1, maximum is 3
            test:
                '#and':
                -   sequence_number: {'#gte': '1'}
                -   sequence_number: {'#lte': '3'}
    - !mobyle/inputprogramparameter
        prompt: G+C content of the output sequences
        format: ( "" , " -g " + str(value) + " ")[value is not None and value != vdef
            ]
        name: gc_content
        command: false
        type: !mobyle/floattype {default: 50.9}
        ctrls:
        -   message: minimum is 0, maximum is 100
            test:
                '#and':
                -   gc_content: {'#gte': '0'}
                -   gc_content: {'#lte': '100'}
    - !mobyle/inputprogramparameter
        comment: A list of codons not to incorporate in the output sequences (typically
            codons rarely used in the genome).
        prompt: Forbidden codons (comma-separated list)
        format: ( "" , " -f " + value + " ")[value is not None and value != vdef ]
        name: forbidden_codons
        command: false
        type: !mobyle/stringtype {default: 'CTG,AGG,ATA,TAG'}
    - !mobyle/inputprogramparameter
        comment: <html:div xmlns:html="http://www.w3.org/1999/xhtml">For a description
            of the CAI, please refer to the<html:a href="http://www.ncbi.nlm.nih.gov/pubmed/3547335"
            target="_blank">original article</html:a>. This option overrides any specified
            G+C content value.</html:div>
        prompt: Force to maximize Codon Adaptation Index of the generated sequence
            (with respect to E. coli)
        format: ( "" , " -c" )[ value ]
        name: force_max_cai
        command: false
        type: !mobyle/booleantype {default: false}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter
        prompt: Report
        filenames: '"stat.txt"'
        name: elp_report
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Sequences
        filenames: '"sequences.fas"'
        name: sequences
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:2200']
            data_terms: ['EDAM_data:2977']
    - !mobyle/outputprogramparameter {prompt: Evolutionary landscape comparison, filenames: '"landscapes.png"',
        name: graphic_report}
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"elp.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"elp.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
comment: "<html:div xmlns:html=\"http://www.w3.org/1999/xhtml\"><html:p>This software\
    \ and its underlying principle are covered by copyright laws and by the international\
    \ patent application WO/2006/046132.</html:p><html:p>Their use are exclusively\
    \ authorized for academic purpose.\n\t\t\tAcademic users are kindly requested\
    \ to cite this source when referring to said software.\n\t\t\tFor any use other\
    \ than academic, please contact<html:a href=\"mailto:christian.mally@pasteur.fr\"\
    >Christian Mally</html:a>at the Technology Transfer Service of the Pasteur Institute.</html:p></html:div>"
references:
- {doi: null, label: '<html:a xmlns:html="http://www.w3.org/1999/xhtml" href="http://dx.doi.org/10.1371%2Fjournal.pgen.1000256"
        target="_blank">Cambray G, Mazel D 2008 Synonymous Genes Explore Different
        Evolutionary Landscapes. PLoS Genetics 4(11): e1000256 doi:10.1371/journal.pgen.1000256</html:a>',
    url: null}
command: elp
env: {}