comalign.yaml

!mobyle/program
name: comalign
title: ComAlign
description: is a program, that given a number of sequences generates a number of
    heuristic alignments and combines these best possible.
authors: O. Caprani, K. Bucka-Lassen
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter
        comment: the sequences must be in the GenAl format
        prompt: Sequences File (-f)
        format: '" -f" + str(value)'
        simple: true
        argpos: 1
        mandatory: true
        name: seq
        command: false
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2044']
    - !mobyle/inputprogramparameter
        prompt: Random seed number (-s)
        format: ( "" , " -s" + str(value) )[ value is not None and value != vdef]
        argpos: 1
        name: seed
        command: false
        type: !mobyle/integertype {default: 1}
    - !mobyle/inputprogramparameter
        prompt: Number of sequences that are to be aligned (-n)
        format: ( "" , " -n" + str(value) )[ value is not None and value != vdef]
        argpos: 1
        name: seqnb
        command: false
        type: !mobyle/integertype {default: 2}
    - !mobyle/inputprogramparameter
        comment: On each iteration a new alignment is added to the pool of alignments
            ComAlign is working on
        prompt: Number of iterations (-i)
        format: ( "" , " -i" + str(value) )[ value is not None and value != vdef]
        argpos: 1
        name: iterations
        command: false
        type: !mobyle/integertype {default: 10}
    - !mobyle/inputprogramparameter
        prompt: 'Score: ComAlign records the time it took to find a solution as good
            as this score (-l)'
        format: ( "" , " -l" + str(value) )[ value is not None]
        argpos: 1
        name: score
        command: false
        type: !mobyle/integertype {}
    - !mobyle/inputprogramparameter
        prompt: ComAlign marks the best solution found after this number of 1/100
            seconds (-t)
        format: ( "" , " -t" + str(value) )[ value is not None ]
        argpos: 1
        name: time
        command: false
        type: !mobyle/integertype {}
    - !mobyle/inputprogramparameter
        prompt: Makes ComAlign terminate if the score hasn't changed within the last
            this number of iterations (-c)
        format: ( "" , " -c" + str(value) )[ value is not None and value != vdef]
        argpos: 1
        name: last_iterations
        command: false
        type: !mobyle/integertype {default: 20}
    - !mobyle/inputprogramparameter
        prompt: Print the best found alignment on termination (-a)
        format: ( "" , " -a" )[ value ]
        argpos: 1
        name: print_best
        command: false
        type: !mobyle/booleantype {default: false}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"comalign.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"comalign.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0498']
topics: ['EDAM_topic:0182']
documentation_links: ['http://www.daimi.au.dk/~ocaprani/ComAlign/HowTo.html']
homepage_links: ['http://www.daimi.au.dk/~ocaprani/ComAlign/ComAlign.html']
command: ComAlign
env: {}
source_links: ['http://www.daimi.au.dk/~ocaprani/ComAlign/programs/']