clique.yaml

!mobyle/program
name: clique
title: clique
description: Compatibility Program
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter
        format: '"clique < clique.params"'
        argpos: 0
        name: clique
        command: true
        hidden: true
        type: !mobyle/stringtype {}
    - !mobyle/inputprogramparameter
        prompt: Input File
        format: '"ln -s "+ str( infile ) + " infile && "'
        simple: true
        argpos: -10
        mandatory: true
        name: infile
        precond:
            infile: {'#ne': infile}
        command: false
    - !mobyle/inputprogramparagraph
        prompt: Clique options
        name: clique_opt
        children:
        - !mobyle/inputprogramparameter
            comment: "There should also be, in the input file after the numbers of\
                \ species and characters, an A on the first line of the file. There\
                \ must also be, before the character data, a line or lines giving\
                \ the ancestral states for each character. It will look like the data\
                \ for a species (the ancestor). It must start with the letter A in\
                \ the first column. There then follow enough characters or blanks\
                \ to complete the full length of a species name (e. g. ANCESTOR).\
                \ Then the states which are\n              ancestral for the individual\
                \ characters follow. These may be 0, 1 or ?, the latter indicating\
                \ that the ancestral state is unknown.Examples:ANCESTOR 0010011"
            prompt: Use ancestral states in input file (A)
            format: ( "" , "A\n" )[ value ]
            argpos: 1
            paramfile: clique.params
            name: use_ancestral_state
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Specify minimum clique size? (C)
            format: ( "" , "C\n"+ str( min_clique_size ) + "\n")[ value ]
            argpos: 3
            paramfile: clique.params
            name: spec_min_clique_size
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: This option indicates that you wish to specify a minimum clique
                size and print out all cliques (and their associated trees) greater
                than or equal to than that size.
            prompt: Minimum clique size
            format: '""'
            argpos: 2
            paramfile: clique.params
            mandatory: true
            name: min_clique_size
            precond: spec_min_clique_size
            command: false
            type: !mobyle/integertype {}
    - !mobyle/inputprogramparagraph
        prompt: Bootstrap options
        name: bootstrap
        children:
        - !mobyle/inputprogramparameter
            prompt: Analyze multiple data sets (M)
            format: ( "" , "M\nD\n"+ str( datasets_number ) +"\n" )[ value ]
            argpos: 10
            paramfile: clique.params
            name: multiple_dataset
            precond: {'#not': multiple_dataweights}
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: How many data sets (D)
            format: '""'
            argpos: 9
            mandatory: true
            name: datasets_number
            precond: multiple_dataset
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            prompt: Compute a consensus tree
            format: ( "", " && cp infile clique.infile &&  cp clique.outtree intree
                && consense <consense.params && mv outtree consense.outtree && mv
                outfile consense.outfile" )[ value ]
            argpos: 10
            name: consense
            precond:
                '#and': [multiple_dataset, print_treefile]
            command: false
            type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparagraph
        prompt: Weigth options
        name: weigths
        children:
        - !mobyle/inputprogramparameter
            prompt: Sites weighted? (W)
            format: ( "" , "W\n" )[ value ]
            argpos: 19
            paramfile: clique.params
            name: site_weigthed
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Analyze multiple data Weigths (M)
            format: ( "" , "M\nW\n"+ str( dataweights_number ) +"\n" )[ value ]
            argpos: 20
            paramfile: clique.params
            name: multiple_dataweights
            precond: {'#not': multiple_dataset}
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: How many sets of weights?
            format: '""'
            argpos: 21
            mandatory: true
            name: dataweights_number
            precond: multiple_dataweights
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            prompt: Weight file
            format: '" ln -s " + str( value ) +" weights && "'
            argpos: -20
            mandatory: true
            name: weigth_file
            precond:
                '#or': [site_weigthed, multiple_dataweights]
            command: false
    - !mobyle/inputprogramparagraph
        prompt: Output options
        name: output
        children:
        - !mobyle/inputprogramparameter
            prompt: Print out compatibility matrix (3)
            format: ( "" , "3\n" )[ value ]
            argpos: 1
            paramfile: clique.params
            name: print_matrix
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: Tells the program to print a semi-graphical picture of the tree
                in the outfile.
            prompt: Print out tree (4)
            format: ( "4\n" , "" )[ value ]
            argpos: 1
            paramfile: clique.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 (5)
            format: ( "5\n" , "" )[ value ]
            argpos: 1
            paramfile: clique.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: clique.params
            name: printdata
            command: false
            type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparagraph
        prompt: Other options
        name: other_options
        children:
        - !mobyle/inputprogramparameter
            prompt: Outgroup root (O)
            format: ("" , "O\\n%s\\n" % str(value) )[ value is not None and value
                != vdef ]
            argpos: 1
            paramfile: clique.params
            name: outgroup
            command: false
            type: !mobyle/integertype {default: 1}
    - !mobyle/inputprogramparameter
        format: '"Y\n"'
        argpos: 1000
        paramfile: clique.params
        name: confirm
        command: false
        hidden: true
        type: !mobyle/stringtype {}
    - !mobyle/inputprogramparameter
        format: '"0\n"'
        argpos: -1
        paramfile: clique.params
        name: terminal_type
        command: false
        hidden: true
        type: !mobyle/stringtype {}
    - !mobyle/inputprogramparameter
        format: '"Y\n"'
        argpos: 1000
        paramfile: consense.params
        name: consense_confirm
        precond: consense
        command: false
        hidden: true
        type: !mobyle/stringtype {}
    - !mobyle/inputprogramparameter
        format: '"T\n"'
        argpos: -2
        paramfile: consense.params
        name: consense_terminal_type
        precond: consense
        command: false
        hidden: true
        type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter {prompt: Output file, filenames: '"clique.outfile"',
        name: outfile}
    - !mobyle/outputprogramparameter
        prompt: Output tree
        filenames: '"clique.outtree"'
        name: treefile
        precond: print_treefile
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:1910']
            data_terms: ['EDAM_data:0872']
    - !mobyle/outputprogramparameter {prompt: Consense output file, filenames: '"consense.outfile"',
        name: consense_outfile, precond: consense}
    - !mobyle/outputprogramparameter
        prompt: Consense output tree
        filenames: '"consense.outtree"'
        name: consense_treefile
        precond: consense
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:1910']
            data_terms: ['EDAM_data:0872']
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"clique.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"clique.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
comment: 'This program uses the compatibility method for unrooted two-state characters
    to obtain the largest cliques of characters and the trees

    which they suggest.'
operations: ['EDAM_operation:0546']
topics: ['EDAM_topic:0084']
documentation_links: ['http://bioweb2.pasteur.fr/docs/phylip/doc/clique.html']
env: {}