consense.yaml

!mobyle/program
name: consense
title: consense
description: Consensus tree program
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter
        format: '"consense <consense.params"'
        argpos: 0
        name: consense
        command: true
        hidden: true
        type: !mobyle/stringtype {}
    - !mobyle/inputprogramparameter
        comment: Input is a tree file which contains a series of trees in the Newick
            standard form
        prompt: Series of trees in file (intree)
        format: '"ln -s "+ str( infile )+ " intree &&"'
        simple: true
        argpos: -10
        mandatory: true
        name: infile
        command: false
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:1910']
            data_terms: ['EDAM_data:0872']
    - !mobyle/inputprogramparameter
        prompt: Consensus type
        paramfile: consense.params
        name: type
        command: false
        type: !mobyle/stringtype {default: MRE}
    - !mobyle/inputprogramparagraph
        prompt: Output options
        name: output
        children:
        - !mobyle/inputprogramparameter
            comment: Tells the program to print a semi-graphical picture of the tree
                in the outfile.
            prompt: Print out tree (3)
            format: ( "3\n" , "" )[ value ]
            argpos: 1
            paramfile: consense.params
            name: print_tree
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: Tells the program to save the tree in a treefile (a standard
                representation of trees where the tree is specified by a nested pairs
                of parentheses, enclosing names and separated by commas).
            prompt: Write out trees onto tree file (4)
            format: ( "4\n" , "" )[ value ]
            argpos: 1
            paramfile: consense.params
            name: print_treefile
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Print out the data at start of run (1)
            format: ( "" , "1\n" )[ value ]
            argpos: 1
            paramfile: consense.params
            name: printdata
            command: false
            type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparagraph
        prompt: Other options
        name: other_options
        children:
        - !mobyle/inputprogramparameter
            prompt: Outgroup species (O)
            format: ( "" , "O\n"+ str( value ) +"\n" )[ value is not None and value
                != vdef ]
            argpos: 1
            paramfile: consense.params
            name: outgroup
            command: false
            type: !mobyle/integertype {default: 1}
        - !mobyle/inputprogramparameter
            prompt: Trees to be treated as rooted (R)
            format: ( "" , "R\n" )[ value ]
            argpos: 1
            paramfile: consense.params
            name: rooted
            command: false
            type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparameter
        format: '"Y\n"'
        argpos: 1000
        paramfile: consense.params
        name: confirm
        command: false
        hidden: true
        type: !mobyle/stringtype {}
    - !mobyle/inputprogramparameter
        format: '"T\n"'
        argpos: -1
        paramfile: consense.params
        name: terminal_type
        command: false
        hidden: true
        type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter {prompt: Consense output file, filenames: '"consense.outfile"',
        argpos: 40, name: outfile}
    - !mobyle/outputprogramparameter
        prompt: Consense tree file
        filenames: '"consense.outtree"'
        argpos: 50
        name: treefile
        precond: print_treefile
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:1910']
            data_terms: ['EDAM_data:0872']
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"consense.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"consense.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
comment: "CONSENSE reads a  file of  computer-readable trees\n\tand prints out (and\
    \ may also write out onto a file) a consensus tree."
operations: ['EDAM_operation:0555']
topics: ['EDAM_topic:0084']
documentation_links: ['http://bioweb2.pasteur.fr/docs/phylip/doc/consense.html']
env: {}