combat_1.0.yaml

!mobyle/program
name: combat
version: '1.0'
title: COMBAT
description: Comparison of coding DNA
authors: Pedersen, Lyngso,Hein
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter
        format: '"cat " + str(sequence2) + " " + str(sequence1) + " >> sequence.data
            && combat combat.params > distance.out && combine sequence.data combat.aln"'
        argpos: 0
        name: combat
        precond:
            '#and':
            -   sequence1: {'#ne': None}
            -   sequence2: {'#ne': None}
        command: true
        hidden: true
        type: !mobyle/stringtype {}
    - !mobyle/inputprogramparameter
        comment: Sequences must describe an integer number of codon, i.e. the length
            of sequence must be a multiple of three.
        prompt: First Sequence
        format: '''>inputfile\n"sequence.data"\n'''
        simple: true
        argpos: 1
        paramfile: combat.params
        mandatory: true
        name: sequence1
        command: false
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:2200']
            data_terms: ['EDAM_data:2044']
    - !mobyle/inputprogramparameter
        comment: Sequences must describe an integer number of codon, i.e. the length
            of sequence must be a multiple of three.
        prompt: Second Sequence
        simple: true
        mandatory: true
        name: sequence2
        command: false
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:2200']
            data_terms: ['EDAM_data:2044']
    - !mobyle/inputprogramparameter
        prompt: Amino-acid distance matrix
        format: '">distance matrix\n\"/path/to/combat/matrix" + str(value) + ''"\n'''
        argpos: 3
        paramfile: combat.params
        mandatory: true
        name: protein_distance_matrix
        command: false
        type: !mobyle/stringtype
            default: Blosum62_distance.m
            options:
            - {label: PAM60, value: PAM60_distance.m}
            - {label: PAM120, value: PAM120_distance.m}
            - {label: PAM250, value: PAM250_distance.m.m}
            - {label: PAM350, value: PAM350_distance.m}
            - {label: Blosum30, value: Blosum30_distance.m}
            - {label: Blosum62, value: Blosum62_distance.m}
            - {label: Blosum90, value: Blosum90_distance.m}
    - !mobyle/inputprogramparameter
        prompt: Nucleotid distance matrix
        format: '">nucleotide matrix\n\"/path/to/combat/matrix" + str(value) + ''"\n'''
        argpos: 4
        paramfile: combat.params
        mandatory: true
        name: nucleotide_distance_matrix
        command: false
        type: !mobyle/stringtype
            default: nucleotide_distance1.m
            options:
            - {label: Matrix 1, value: nucleotide_distance1.m}
            - {label: Matrix 2, value: nucleotide_distance2.m}
            - {label: Matrix 3, value: nucleotide_distance3.m}
    - !mobyle/inputprogramparameter
        prompt: Gap open cost for protein
        format: '">gap functions\nprotein:        " + str(value)'
        simple: true
        argpos: 5
        paramfile: combat.params
        mandatory: true
        name: protein_gap_open
        command: false
        type: !mobyle/integertype {default: 20}
    - !mobyle/inputprogramparameter
        prompt: Gap extension cost for protein
        format: '" + " + str(value) + "*k\n"'
        simple: true
        argpos: 6
        paramfile: combat.params
        mandatory: true
        name: protein_gap_ext
        command: false
        type: !mobyle/integertype {default: 8}
    - !mobyle/inputprogramparameter
        prompt: Gap open cost for dna
        format: '"dna:        " + str(value)'
        simple: true
        argpos: 7
        paramfile: combat.params
        mandatory: true
        name: dna_gap_open
        command: false
        type: !mobyle/integertype {default: 8}
    - !mobyle/inputprogramparameter
        prompt: Gap extension cost for dna
        format: '" + " + str(value) + "*k"'
        simple: true
        argpos: 8
        paramfile: combat.params
        mandatory: true
        name: dna_gap_ext
        command: false
        type: !mobyle/integertype {default: 2}
    - !mobyle/inputprogramparameter
        format: '" && gnuplot <gnuplot.params"'
        argpos: 100
        name: gnuplot_call
        command: false
        hidden: true
        type: !mobyle/stringtype {}
    - !mobyle/inputprogramparameter
        format: '''set xtics 12,5.,1000\nset ytics 12,5.,1000\nset grid\nset terminal
            postscript\nset output "combat.ps"\nplot "combat.aln" with lines\n'''
        argpos: 1
        paramfile: gnuplot.params
        name: gnuplot_commands
        command: false
        hidden: true
        type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter {prompt: Output file, filenames: '"combat.aln"',
        argpos: 2, name: output_aln}
    - !mobyle/outputprogramparameter
        prompt: Alignment file
        filenames: '"combat.out"'
        name: combat_out
        output_type: stdout
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:2200']
            data_terms: ['EDAM_data:0863']
    - !mobyle/outputprogramparameter {prompt: Distance file, filenames: '"distance.out"',
        name: distance_files}
    - !mobyle/outputprogramparameter {prompt: Postscript file, filenames: '"combat.ps"',
        name: ps_files}
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"combat.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
references:
- {doi: null, label: 'Christian N. S. Pedersen, Rune B. Lyngso and Jotun Hein. Comparison
        of coding DNA in Proceedings of the 9th Annual Symposium of Combinatorial
        Pattern Matching (CPM), 1998.', url: null}
homepage_links: ['http://www.daimi.au.dk/~cstorm/combat/']
env: {}
source_links: ['http://www.daimi.au.dk/~cstorm/combat/']