clustalw-profile.yaml

!mobyle/program
name: clustalw-profile
title: 'Clustalw: Profile alignments'
description: Merge two alignments by profile alignment
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparagraph
        comment: "By PROFILE ALIGNMENT, we mean alignment using\n\t    existing alignments.\
            \ Profile alignments allow you to store\n\t    alignments of your favorite\
            \ sequences and add new sequences to\n\t    them in small bunches at a\
            \ time.  (e.g. an alignment output\n\t    file from CLUSTAL W). One or\
            \ both sets of input sequences may\n\t    include secondary structure\
            \ assignments or gap penalty masks to\n\t    guide the alignment.Merge\
            \ 2 alignments by profile alignment"
        prompt: Profile Alignments parameters
        name: profile
        argpos: 2
        children:
        - !mobyle/inputprogramparameter
            prompt: Profile 1
            format: ( "" , " -profile1=" + str( value ) )[value is not None]
            simple: true
            mandatory: true
            name: profile1
            command: false
            type: !mobyle/formattedtype
                format_terms: ['EDAM_format:1982']
                data_terms: ['EDAM_data:0863']
        - !mobyle/inputprogramparameter
            prompt: Profile 2
            format: ( "" , " -profile2=" + str( value ) )[value is not None]
            simple: true
            mandatory: true
            name: profile2
            command: false
            type: !mobyle/formattedtype
                format_terms: ['EDAM_format:1982']
                data_terms: ['EDAM_data:0863']
        - !mobyle/inputprogramparameter
            prompt: File for old guide tree for profile1 (-usetree1)
            format: ( "" , " -usetree1=" + str( value ))[value is not None]
            name: usetree1
            command: false
            type: !mobyle/formattedtype
                format_terms: ['EDAM_format:1910']
                data_terms: ['EDAM_data:0872']
        - !mobyle/inputprogramparameter
            prompt: File for old guide tree for profile2 (-usetree2)
            format: ( "" , " -usetree2=" + str( value ))[value is not None]
            name: usetree2
            command: false
            type: !mobyle/formattedtype
                format_terms: ['EDAM_format:1910']
                data_terms: ['EDAM_data:0872']
    - !mobyle/inputprogramparagraph
        prompt: General settings
        name: general_settings
        argpos: 3
        children:
        - !mobyle/inputprogramparameter
            prompt: Protein or DNA (-type)
            format: ("", " -type="+str(value))[value is not None]
            name: typeseq
            command: false
            type: !mobyle/stringtype
                default: auto
                options:
                - {label: Automatic, value: auto}
                - {label: Protein, value: protein}
                - {label: DNA, value: dna}
        - !mobyle/inputprogramparameter
            comment: 'slow: by dynamic programming (slow but accurate)fast: method
                of Wilbur and Lipman (extremely fast but approximate)'
            prompt: Toggle Slow/Fast pairwise alignments (-quicktree)
            format: ( "" , " -quicktree")[ value == "fast"]
            simple: true
            name: quicktree
            command: false
            type: !mobyle/stringtype
                default: slow
                options:
                - {label: Slow, value: slow}
                - {label: Fast, value: fast}
    - !mobyle/inputprogramparagraph
        comment: "These similarity scores are calculated from fast,\n\t  approximate,\
            \ global alignments, which are controlled by 4\n\t  parameters. 2 techniques\
            \ are used to make these alignments very\n\t  fast: 1) only exactly matching\
            \ fragments (k-tuples) are\n\t  considered; 2) only the 'best' diagonals\
            \ (the ones with most\n\t  k-tuple matches) are used."
        prompt: Fast Pairwise Alignments parameters
        name: fastpw
        precond: {quicktree: fast}
        argpos: 2
        children:
        - !mobyle/inputprogramparameter
            comment: 'K-TUPLE SIZE: This is the size of exactly matching fragment
                that is used. INCREASE for speed (max= 2 for proteins; 4 for DNA),
                DECREASE for sensitivity. For longer sequences (e.g. >1000 residues)
                you may need to increase the default.'
            prompt: Word size (-ktuple)
            format: ( "" , " -ktuple=" + str( value ) )[value is not None and value
                != vdef ]
            argpos: 2
            name: ktuple
            command: false
            type: !mobyle/integertype {default: 1}
        - !mobyle/inputprogramparameter
            comment: "The number of k-tuple matches on each\n\t\tdiagonal (in an imaginary\
                \ dot-matrix plot) is\n\t\tcalculated. Only the best ones (with most\
                \ matches) are used\n\t\tin the alignment. This parameter specifies\
                \ how\n\t\tmany. Decrease for speed; increase for sensitivity."
            prompt: Number of best diagonals (-topdiags)
            format: ( "" , " -topdiags=" + str( value ))[value is not None and value
                != vdef ]
            argpos: 2
            name: topdiags
            command: false
            type: !mobyle/integertype {default: 5}
        - !mobyle/inputprogramparameter
            comment: "WINDOW SIZE: This is the number of\n\t\tdiagonals around each\
                \ of the 'best' diagonals that will be\n\t\tused. Decrease for speed;\
                \ increase for sensitivity"
            prompt: Window around best diags (-window)
            format: ( "" , " -window=" + str( value ) )[ value is not None and value
                != vdef ]
            argpos: 2
            name: window
            command: false
            type: !mobyle/integertype {default: 5}
        - !mobyle/inputprogramparameter
            comment: "This is a penalty for each gap in the fast\n\t\talignments.\
                \ It has little affect on the speed or\n\t\tsensitivity except for\
                \ extreme values."
            prompt: Gap penalty (-pairgap)
            format: ( "" , " -pairgap=" + str( value ))[ value is not None and value
                != vdef ]
            argpos: 2
            name: pairgap
            command: false
            type: !mobyle/floattype {default: 3.0}
        - !mobyle/inputprogramparameter
            prompt: Percent or absolute score ? (-score)
            format: ( "" , " -score=" +str( value ) )[value is not None and value
                !=vdef]
            argpos: 2
            name: score
            command: false
            type: !mobyle/stringtype
                default: percent
                options:
                - {label: Percent, value: percent}
                - {label: Absolute, value: absolute}
    - !mobyle/inputprogramparagraph
        comment: "These parameters do not have any affect on the\n\t  speed of the\
            \ alignments. They are used to give initial alignments\n\t  which are\
            \ then rescored to give percent identity scores. These %\n\t  scores are\
            \ the ones which are displayed on the screen. The scores\n\t  are converted\
            \ to distances for the trees."
        prompt: Slow Pairwise Alignments parameters
        name: slowpw
        precond: {quicktree: slow}
        argpos: 2
        children:
        - !mobyle/inputprogramparameter
            prompt: Gap opening penalty (-pwgapopen)
            format: ( "" , " -pwgapopen=" + str( value ) )[ value is not None and
                value != vdef ]
            name: pwgapopen
            command: false
            type: !mobyle/floattype {default: 10.0}
        - !mobyle/inputprogramparameter
            prompt: Gap extension penalty (-pwgapext)
            format: ( "" , " -pwgapext=" + str( value ) )[ value is not None and value
                != vdef ]
            name: pwgapext
            command: false
            type: !mobyle/floattype {default: 0.1}
        - !mobyle/inputprogramparagraph
            prompt: Protein parameters
            name: slowpw_prot
            precond: {typeseq: protein}
            children:
            - !mobyle/inputprogramparameter
                comment: "The scoring table which describes the\n\t\tsimilarity of\
                    \ each amino acid to each other. For DNA, an\n\t\tidentity matrix\
                    \ is used.BLOSUM (Henikoff). These matrices appear to\n\t\tbe\
                    \ the best available for carrying out data base similarity\n\t\
                    \t(homology searches). The matrices used are: Blosum80, 62,\n\t\
                    \t40 and 30.The Gonnet Pam 250 matrix has been reported\n\t\t\
                    as the best single matrix for alignment, if you only choose\n\t\
                    \tone matrix. Our experience with profile database searches\n\t\
                    \tis that the Gonnet series is unambiguously superior to the\n\
                    \t\tBlosum series at high divergence. However, we did not get\n\
                    \t\tthe series to perform systematically better than the Blosum\n\
                    \t\tseries in Clustal W (communication of the authors).PAM (Dayhoff).\
                    \ These have been extremely\n\t\twidely used since the late '70s.\
                    \ We use the PAM 120, 160,\n\t\t250 and 350 matrices."
                prompt: Protein weight matrix (-pwmatrix)
                format: ( "" , " -pwmatrix=" + str(value) )[value is not None and
                    value != vdef ]
                name: pwmatrix
                command: false
                type: !mobyle/stringtype
                    default: gonnet
                    options:
                    - {label: BLOSUM30 (Henikoff), value: blosum}
                    - {label: Gonnet 250, value: gonnet}
                    - {label: PAM350 (Dayhoff), value: pam}
                    - {label: Identity matrix, value: id}
        - !mobyle/inputprogramparagraph
            prompt: DNA parameters
            name: slowpw_dna
            precond: {typeseq: dna}
            children:
            - !mobyle/inputprogramparameter
                comment: "For DNA, a single matrix (not a series) is\n\t\tused. Two\
                    \ hard-coded matrices are available:1) IUB. This is the default\
                    \ scoring matrix\n\t\tused by BESTFIT for the comparison of nucleic\
                    \ acid\n\t\tsequences. X's and N's are treated as matches to any\
                    \ IUB\n\t\tambiguity symbol. All matches score 1.9; all mismatches\
                    \ for\n\t\tIUB symbols score 0.2) CLUSTALW(1.6). The previous\
                    \ system used\n\t\tby ClustalW, in which matches score 1.0 and\
                    \ mismatches\n\t\tscore 0. All matches for IUB symbols also score\
                    \ 0."
                prompt: DNA weight matrix (-pwdnamatrix)
                format: ( "" , " -pwdnamatrix=" + str(value) )[ value is not None
                    and value != vdef ]
                name: pwdnamatrix
                command: false
                type: !mobyle/stringtype
                    default: iub
                    options:
                    - {label: IUB, value: iub}
                    - {label: CLUSTALW, value: clustalw}
    - !mobyle/inputprogramparagraph
        comment: "These options, when doing a profile alignment,\n\t  allow you to\
            \ set 2D structure parameters. If a solved structure\n\t  is available,\
            \ it can be used to guide the alignment by raising\n\t  gap penalties\
            \ within secondary structure elements, so that gaps\n\t  will preferentially\
            \ be inserted into unstructured surface\n\t  loops. Alternatively, a user-specified\
            \ gap penalty mask can be\n\t  supplied directly.A gap penalty mask is\
            \ a series of numbers between\n\t  1 and 9, one per position in the alignment.\
            \ Each number specifies\n\t  how much the gap opening penalty is to be\
            \ raised at that position\n\t  (raised by multiplying the basic gap opening\
            \ penalty by the\n\t  number) i.e. a mask figure of 1 at a position means\
            \ no change in\n\t  gap opening penalty; a figure of 4 means that the\
            \ gap opening\n\t  penalty is four times greater at that position, making\
            \ gaps 4\n\t  times harder to open.Gap penalty masks is to be supplied\
            \ with the\n\t  input sequences. The masks work by raising gap penalties\
            \ in\n\t  specified regions (typically secondary structure elements) so\n\
            \t  that gaps are preferentially opened in the less well conserved\n\t\
            \  regions (typically surface loops).CLUSTAL W can read the masks from\
            \ SWISS-PROT,\n\t  CLUSTAL or GDE format input files. For many 3-D protein\n\
            \t  structures, secondary structure information is recorded in the\n\t\
            \  feature tables of SWISS-PROT database entries. You should always\n\t\
            \  check that the assignments are correct - some are quite\n\t  inaccurate.\
            \ CLUSTAL W looks for SWISS-PROT HELIX and STRAND\n\t  assignments e.g.FT\
            \   HELIX       100    115FT   HELIX       100    115The structure and\
            \ penalty masks can also be read from CLUSTAL alignment format as comment\
            \ lines beginning !SS_ or GM_ e.g.!SS_HBA_HUMA    ..aaaAAAAAAAAAAaaa.aaaAAAAAAAAAAaaaaaaAaaa.........aaaAAAAAA!GM_HBA_HUMA\
            \    112224444444444222122244444444442222224222111111111222444444HBA_HUMA\
            \        VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKNote\
            \ that the mask itself is a set of numbers between 1 and 9 each of which\
            \ is assigned to the residue(s) in the same column below. In GDE flat\
            \ file format, the masks are specified as text and the names must begin\
            \ with SS_ or GM_. Either a structure or penalty mask or both may be used.\
            \ If both are included in an alignment, the user will be asked which is\
            \ to be used."
        prompt: Structure Alignments parameters
        name: structure
        argpos: 2
        children:
        - !mobyle/inputprogramparameter
            comment: This option controls whether the input secondary structure information
                or gap penalty masks will be used.
            prompt: Do not use secondary structure-gap penalty mask for profile 1
                (-nosecstr1)
            format: ( "" , " -nosecstr1")[ value ]
            argpos: 2
            name: nosecstr1
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: This option controls whether the input secondary structure information
                or gap penalty masks will be used.
            prompt: Do not use secondary structure-gap penalty mask for profile 2
                (-nosecstr2)
            format: ( "" , " -nosecstr2")[ value ]
            name: nosecstr2
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: "This option provides the value for raising\n\t\tthe gap penalty\
                \ at core Alpha Helical (A) residues. In\n\t\tCLUSTAL format, capital\
                \ residues denote the A and B core\n\t\tstructure notation. The basic\
                \ gap penalties are multiplied\n\t\tby the amount specified."
            prompt: Helix gap penalty (-helixgap)
            format: ( "" , " -helixgap=" + str( value ) )[ value is not None and value
                != vdef ]
            name: helixgap
            command: false
            type: !mobyle/integertype {default: 4}
        - !mobyle/inputprogramparameter
            comment: "This option provides the value for raising\n\t\tthe gap penalty\
                \ at Beta Strand (B) residues. In CLUSTAL\n\t\tformat, capital residues\
                \ denote the A and B core structure\n\t\tnotation. The basic gap penalties\
                \ are multiplied by the\n\t\tamount specified."
            prompt: Strand gap penalty (-strandgap)
            format: ( "" , " -strandgap=" + str( value ) )[ value is not None and
                value != vdef ]
            name: strandgap
            command: false
            type: !mobyle/integertype {default: 4}
        - !mobyle/inputprogramparameter
            comment: "This option provides the value for the gap\n\t\tpenalty in Loops.\
                \ By default this penalty is not raised. In\n\t\tCLUSTAL format, loops\
                \ are specified by . in the secondary\n\t\tstructure notation."
            prompt: Loop gap penalty (-loopgap)
            format: ( "" , " -loopgap=" + str( value ) )[ value is not None and value
                != vdef ]
            name: loopgap
            command: false
            type: !mobyle/integertype {default: 1}
        - !mobyle/inputprogramparameter
            comment: "This option provides the value for setting\n\t\tthe gap penalty\
                \ at the ends of secondary structures. Ends\n\t\tof secondary structures\
                \ are observed to grow and-or shrink\n\t\tin related structures. Therefore\
                \ by default these are given\n\t\tintermediate values, lower than\
                \ the core penalties. All\n\t\tsecondary structure read in as lower\
                \ case in CLUSTAL format\n\t\tgets the reduced terminal penalty."
            prompt: Secondary structure terminal penalty (-terminalgap)
            format: ( "" , " -terminalgap=" + str( value ) )[ value is not None and
                value != vdef ]
            name: terminalgap
            command: false
            type: !mobyle/integertype {default: 2}
        - !mobyle/inputprogramparameter
            comment: "This option (together with the -helixendin)\n\t\tspecify the\
                \ range of structure termini for the intermediate\n\t\tpenalties.\
                \ In the alignment output, these are indicated as\n\t\tlower case.\
                \ For Alpha Helices, by default, the range spans\n\t\tthe end helical\
                \ turn."
            prompt: 'Helix terminal positions:  number of residues inside helix to
                be treated as terminal (-helixendin)'
            format: ( "" , " -helixendin=" + str( value ) )[ value is not None and
                value != vdef ]
            name: helixendin
            command: false
            type: !mobyle/integertype {default: 3}
        - !mobyle/inputprogramparameter
            comment: "This option (together with the -helixendin)\n\t\tspecify the\
                \ range of structure termini for the intermediate\n\t\tpenalties.\
                \ In the alignment output, these are indicated as\n\t\tlower case.\
                \ For Alpha Helices, by default, the range spans\n\t\tthe end helical\
                \ turn."
            prompt: 'Helix terminal positions: number of residues outside helix to
                be treated as terminal (-helixendout)'
            format: ( "" , " -helixendout=" + str( value ) )[ value is not None and
                value != vdef ]
            name: helixendout
            command: false
            type: !mobyle/integertype {default: 0}
        - !mobyle/inputprogramparameter
            comment: "This option (together with the\n\t\t-strandendout option) specify\
                \ the range of structure\n\t\ttermini for the intermediate penalties.\
                \ In the alignment\n\t\toutput, these are indicated as lower case.\
                \ For Beta\n\t\tStrands, the default range spans the end residue and\
                \ the\n\t\tadjacent loop residue, since sequence conservation often\n\
                \t\textends beyond the actual H-bonded Beta Strand."
            prompt: 'Strand terminal positions: number of residues inside strand to
                be treated as terminal (-strandendin)'
            format: ( "" , " -strandendin=" + str( value ) )[ value is not None and
                value != vdef ]
            name: strandendin
            command: false
            type: !mobyle/integertype {default: 1}
        - !mobyle/inputprogramparameter
            comment: "This option (together with the -strandendin\n\t\toption) specify\
                \ the range of structure termini for the\n\t\tintermediate penalties.\
                \ In the alignment output, these are\n\t\tindicated as lower case.\
                \ For Beta Strands, the default\n\t\trange spans the end residue and\
                \ the adjacent loop residue,\n\t\tsince sequence conservation often\
                \ extends beyond the actual\n\t\tH-bonded Beta Strand."
            prompt: 'Strand terminal positions: number of residues outside strand
                to be treated as terminal (-strandendout)'
            format: ( "" , " -strandendout=" + str( value ) )[ value is not None and
                value != vdef ]
            name: strandendout
            command: false
            type: !mobyle/integertype {default: 1}
        - !mobyle/inputprogramparameter
            comment: "This option lets you choose whether or not\n\t\tto include the\
                \ masks in the CLUSTAL W output\n\t\talignments. Showing both is useful\
                \ for understanding how\n\t\tthe masks work. The secondary structure\
                \ information is\n\t\titself very useful in judging the alignment\
                \ quality and in\n\t\tseeing how residue conservation patterns vary\
                \ with\n\t\tsecondary structure."
            prompt: Output in alignment (-secstrout)
            format: ( "" , " -secstrout=" + str( value ) )[ value is not None and
                value != vdef ]
            name: secstrout
            command: false
            type: !mobyle/stringtype
                default: STRUCTURE
                options:
                - {label: Secondary Structure, value: STRUCTURE}
                - {label: Gap Penalty Mask, value: MASK}
                - {label: Structure and Penalty Mask, value: BOTH}
                - {label: None, value: NONE}
    - !mobyle/inputprogramparagraph
        prompt: Output parameters
        name: outputparam
        argpos: 5
        children:
        - !mobyle/inputprogramparameter
            prompt: Output format (-output)
            format: ( "" , " -output=" + str( value) )[ value is not None and value
                != vdef ]
            name: outputformat
            command: false
            type: !mobyle/stringtype
                default: 'null'
                options:
                - {label: CLUSTAL, value: 'null'}
                - {label: GCG, value: GCG}
                - {label: GDE, value: GDE}
                - {label: PHYLIP, value: PHYLIPI}
                - {label: NEXUS, value: NEXUS}
                - {label: PIR, value: PIR}
                - {label: FASTA, value: FASTA}
        - !mobyle/inputprogramparameter
            prompt: Output sequence numbers in the output file (for clustalw output
                only) (-seqnos)
            format: ( "" , " -seqnos=on")[ value is not None and value != vdef]
            name: seqnos
            precond:
                outputformat: {'#eq': None}
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Result order (-outorder)
            format: ( "" , " -outorder=" + str(value))[ value is not None and value
                != vdef ]
            name: outorder
            command: false
            type: !mobyle/stringtype
                default: aligned
                options:
                - {label: Input, value: input}
                - {label: Aligned, value: aligned}
        - !mobyle/inputprogramparameter
            prompt: Sequence alignment file name (-outfile)
            format: ( "" , " -outfile=" + str( value))[ value is not None ]
            name: outfile
            command: false
            type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparagraph
        prompt: Output parameters
        name: outputparam
        argpos: 5
        children:
        - !mobyle/outputprogramparameter
            prompt: Alignment file
            filenames: ((("*.nxs","*.phy")[outputformat == 'PHYLIPI'],"*.msf")[outputformat
                == 'GCG'],str(outfile))[outfile is not None]
            name: aligfile
            precond:
                outputformat:
                    '#in': [NEXUS, GCG, PHYLIPI]
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:0863']
        - !mobyle/outputprogramparameter
            comment: 'In the conservation line output in the clustal format alignment
                file, three characters are used:''*'' indicates positions which have
                a single, fully conserved residue.'':'' indicates that one of the
                following ''strong'' groups is fully conserved (STA,NEQK,NHQK,NDEQ,QHRK,MILV,MILF,HY,FYW).''.''
                indicates that one of the following ''weaker'' groups is fully conserved
                (CSA,ATV,SAG,STNK,STPA,SGND,SNDEQK,NDEQHK,NEQHRK,FVLIM,HFY).These
                are all the positively scoring groups that occur in the Gonnet Pam250

                matrix. The strong and weak groups are defined as strong score >0.5
                and weak

                score =<0.5 respectively.'
            prompt: Alignment file
            filenames: ("*.aln", str(outfile))[outfile is not None]
            name: clustalaligfile
            precond:
                outputformat: {'#eq': None}
            type: !mobyle/formattedtype
                format_terms: ['EDAM_format:1982']
                data_terms: ['EDAM_data:0863']
        - !mobyle/outputprogramparameter
            prompt: Sequences file
            filenames: ((("*.fasta","*.pir")[outputformat == 'PIR'],"*.gde")[outputformat
                == 'GDE'],str(outfile))[outfile is not None]
            name: seqfile
            precond:
                outputformat:
                    '#in': [GDE, PIR, FASTA]
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/outputprogramparameter
            prompt: Tree file
            filenames: '"*.dnd"'
            name: dndfile
            type: !mobyle/formattedtype
                format_terms: ['EDAM_format:1910']
                data_terms: ['EDAM_data:0872']
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"clustalw-profile.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"clustalw-profile.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0512']
topics: ['EDAM_topic:0080', 'EDAM_topic:0182']
command: clustalw -profile
env: {}