bl2seq.yaml

!mobyle/program
name: bl2seq
title: BL2SEQ
description: Comparison between two sequences with Blast (NCBI)
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter
        prompt: Blast initiation
        format: '"bl2seq"'
        argpos: 1
        name: blast_init
        command: true
        hidden: true
        type: !mobyle/stringtype {}
    - !mobyle/inputprogramparameter
        comment: '- Blastp compares amino acid query sequences- Blastn compares nucleotide
            query sequences- tBlastx compares translated a nucleotide sequence and
            an amino acid sequence- tBlastn compares an amino acid sequence translated
            and a nucleotide sequence- tBlastx compares translated nucleotide sequences'
        prompt: Blast program (-p)
        format: '" -p " + str(value)'
        simple: true
        argpos: 2
        mandatory: true
        name: bl2seq
        command: false
        type: !mobyle/stringtype
            default: 'null'
            options:
            - {label: Choose a program, value: 'null'}
            - {label: Blastp (protein/protein), value: blastp}
            - {label: Blastn (nucleotide/nucleotide), value: blastn}
            - {label: Blastx (translated nucleotide/ protein), value: blastx}
            - {label: tBlastn (protein/translated nucleotide), value: tblastn}
            - {label: tBlastx (translated nucleotide/translated nucleotide), value: tblastx}
    - !mobyle/inputprogramparameter
        prompt: First sequence (-i)
        format: '" -i " + str( value )'
        simple: true
        argpos: 3
        mandatory: true
        name: first_sequence
        command: false
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:2200']
            data_terms: ['EDAM_data:2044']
    - !mobyle/inputprogramparameter
        comment: Location on query sequence
        prompt: Start of required region in first query sequence (-I)
        name: first_start_region
        command: false
        type: !mobyle/integertype {}
    - !mobyle/inputprogramparameter
        prompt: End of required region in first sequence (-I)
        format: ( ' -I "%s "' % (str(first_start_region)), ' -I "%s %s"' % (str(first_start_region),
            str(value)))[value is not None]
        argpos: 3
        name: first_end_region
        precond:
            first_start_region: {'#ne': None}
        command: false
        type: !mobyle/integertype {}
    - !mobyle/inputprogramparameter
        prompt: Second sequence (-j)
        format: '" -j " + str(value)'
        simple: true
        argpos: 4
        mandatory: true
        name: second_sequence
        command: false
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:2200']
            data_terms: ['EDAM_data:2044']
    - !mobyle/inputprogramparameter
        prompt: Start of required region in second sequence (-J)
        argpos: 4
        name: second_start_region
        command: false
        type: !mobyle/integertype {}
    - !mobyle/inputprogramparameter
        prompt: End of required region in second sequence (-J)
        format: ( ' -J "%s "' % (str(second_start_region)), ' -J "%s %s"' % (str(second_start_region),
            str(value)))[value is not None]
        argpos: 4
        name: second_end_region
        precond:
            second_start_region: {'#ne': None}
        command: false
        type: !mobyle/integertype {}
    - !mobyle/inputprogramparagraph
        prompt: Scoring options
        name: scoring_opt
        argpos: 5
        children:
        - !mobyle/inputprogramparameter
            comment: 'Default: 5 for blastn; 10 for blastp, blastx and 11 for tblastn'
            prompt: Cost to open a gap (-G)
            format: ("" , " -G "+str(value) )[value is not None]
            name: open_a_gap
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            comment: 'Default: 2 for blastn; 1 for blastp, blastx and tblastnLimited
                values for gap existence and extension are supported for these programs.Existence
                -- Extension:BLOSUM909 -- 2, 8 -- 2, 7 -- 2, 6 -- 211 -- 1, 10 --
                1, 9 -- 1BLOSUM8025 -- 2, 13 -- 2, 9 -- 2, 8 -- 2, 7 -- 2, 6 -- 211
                -- 1, 10 -- 1, 9 -- 1BLOSUM6211 -- 2, 10 -- 2, 9 -- 2, 8 -- 2, 7 --
                2, 6 -- 213 -- 1, 12 -- 1, 11 -- 1, 10 -- 1, 9 -- 1BLOSUM4513 -- 3,
                12 -- 3, 11 -- 3, 10 -- 316 -- 2, 15 -- 2, 14 -- 2, 13 -- 2, 12 --
                219 -- 1, 18 -- 1, 17 -- 1, 16 -- 1PAM307 -- 2, 6 -- 2, 5 -- 210 --
                1, 9 -- 1, 8 -- 1PAM708 -- 2, 7 -- 2, 6 -- 211 -- 1, 10 -- 1, 9 --
                1'
            prompt: Cost to extend a gap (-E)
            format: ("" , " -E "+str(value) )[value is not None]
            name: extend_a_gap
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparagraph
            prompt: Protein penalty (not for blastn)
            name: scoring_blast
            precond:
                bl2seq: {'#ne': blastn}
            children:
            - !mobyle/inputprogramparameter
                prompt: Similarity matrix (-M)
                format: ("" , " -M "+str(value) )[value is not None and value != vdef]
                name: matrix
                command: false
                type: !mobyle/stringtype
                    default: BLOSUM62
                    options:
                    - {label: BLOSUM90, value: BLOSUM90}
                    - {label: BLOSUM80, value: BLOSUM80}
                    - {label: BLOSUM62, value: BLOSUM62}
                    - {label: BLOSUM50, value: BLOSUM50}
                    - {label: BLOSUM45, value: BLOSUM45}
                    - {label: PAM30, value: PAM30}
                    - {label: PAM70, value: PAM70}
                    - {label: PAM250, value: PAM250}
        - !mobyle/inputprogramparagraph
            prompt: Blastn penalty
            name: scoring_blastn
            precond: {bl2seq: blastn}
            children:
            - !mobyle/inputprogramparameter
                prompt: Penalty for a nucleotide mismatch (-q)
                format: ("" , " -q "+str(value) )[value is not None and value != vdef]
                name: mismatch
                command: false
                type: !mobyle/integertype {default: -3}
            - !mobyle/inputprogramparameter
                prompt: Reward for a nucleotide match (-r)
                format: ("" , " -r "+str(value) )[value is not None and value != vdef]
                name: match
                command: false
                type: !mobyle/integertype {default: 1}
    - !mobyle/inputprogramparagraph
        comment: "Mask off segments of the query sequence that have low compositional\
            \ complexity, as determined by the SEG program of Wootton & Federhen (Computers\
            \ and Chemistry, 1993) or, for BLASTN, by the DUST program of Tatusov\
            \ and Lipman (in preparation). Filtering can eliminate statistically significant\
            \ but biologically uninteresting reports from the blast output (e.g.,\
            \ hits against common acidic-, basic- or proline-rich regions), leaving\
            \ the more biologically interesting regions of the query\n          sequence\
            \ available for specific matching against database sequences.Filtering\
            \ is only applied to the query sequence (or its translation products),\
            \ not to database sequences. Default filtering is DUST for BLASTN, SEG\
            \ for other programs. It is not unusual for nothing at all to be masked\
            \ by SEG, when applied to sequences in SWISS-PROT, so filtering should\
            \ not be expected to always yield an effect. Furthermore, in some cases,\
            \ sequences are masked in their entirety, indicating that the statistical\
            \ significance of any matches reported against the unfiltered\n      \
            \    query sequence should be suspect."
        prompt: Filtering and masking options
        name: filter_opt
        argpos: 6
        children:
        - !mobyle/inputprogramparameter
            prompt: Filter or Masking query sequence (DUST with blastn, SEG with others)
                (-F)
            format: (" -F F" , "")[ value ]
            name: filter
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: A coiled-coiled filter, based on the work of Lupas et al. (Science,
                vol 252, pp. 1162-4 (1991)) written by John Kuzio (Wilson et al.,
                J Gen Virol, vol. 76, pp. 2923-32 (1995))
            prompt: Filtering options (Filter must be true)
            name: other_filters
            precond:
                '#and':
                - filter
                -   other_masking: {'#eq': None}
            command: false
            type: !mobyle/stringtype {default: 'null'}
        - !mobyle/inputprogramparameter
            comment: 'A coiled-coiled filter, based on the work of Lupas et al. (Science,
                vol 252, pp. 1162-4 (1991)) written by John Kuzio (Wilson et al.,
                J Gen Virol, vol. 76, pp. 2923-32 (1995)).It is possible to specify
                that the masking should only be done during the process of building
                the initial words .If the -U option (to mask any lower-case sequence
                in the input FASTA file) is used and one does not wish any other filtering,
                but does wish to mask when building the lookup tables then one should
                specify: -F ''m'''
            prompt: Masking options (Filter must be true)
            name: other_masking
            precond:
                '#and':
                - {filter: '1'}
                -   other_filters: {'#eq': None}
            command: false
            type: !mobyle/stringtype {default: 'null'}
        - !mobyle/inputprogramparameter
            comment: This option specifies that any lower-case letters in the input
                FASTA file should be masked.
            prompt: Use lower case filtering (-U)
            format: ("", " -U T")[value]
            name: lower_case
            command: false
            type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparagraph
        prompt: Selectivity options
        name: selectivity_opt
        argpos: 7
        children:
        - !mobyle/inputprogramparameter
            comment: "The statistical significance threshold for reporting matches\
                \ against database sequences; the default value is 10, such that 10\
                \ matches are expected to be found merely by chance, according to\
                \ the stochastic model of Karlin and Altschul (1990). If the statistical\
                \ significance ascribed to a match is greater than the EXPECT threshold,\
                \ the match will not be reported. Lower EXPECT thresholds are more\
                \ stringent, leading to fewer chance matches being reported. Fractional\
                \ values are\n              acceptable."
            prompt: Expected value (-e)
            format: ("" , " -e "+str(value) )[value is not None and value != vdef]
            simple: true
            name: Expect
            command: false
            type: !mobyle/floattype {default: 10.0}
        - !mobyle/inputprogramparameter
            comment: Use words of size N.Zero invokes default behaviorDefault values:-
                11 for blastn- 3 for others
            prompt: Word Size (-W)
            format: ("" , " -W "+str(value) )[value is not None]
            name: word_size
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            comment: This is the value that control the path graph region explored
                by Blast during a gapped extension (Xg in the NAR paper) (default
                for blastp is 15).Default values:- 30 for blastn- 0 for tblastx- 15
                for others
            prompt: X dropoff value for gapped alignment (-X)
            format: ("" , " -X "+str(value))[value is not None]
            name: dropoff_extent
            command: false
            type: !mobyle/floattype {}
        - !mobyle/inputprogramparameter
            comment: Use zero for the real size
            prompt: Effective length of the search space (-Y)
            format: ("" , " -Y "+str(value) )[value is not None]
            name: eff_len
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            prompt: Perform or not gapped alignment (not available with tblastx) (-g)
            format: (" -g F " , "")[value]
            name: gapped_alig
            precond:
                bl2seq: {'#ne': tblastx}
            command: false
            type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparagraph
        prompt: Translation options
        name: translation_opt
        precond:
            bl2seq:
                '#in': [blastx, tblastx, tblastn]
        argpos: 8
        children:
        - !mobyle/inputprogramparameter
            prompt: Query strand to search against second sequence (for blastx, tblastx
                or tblastn) (-S)
            format: ( "" , " -S " + str(value) )[ value is not None and value!= vdef]
            simple: true
            mandatory: true
            name: strand
            command: false
            type: !mobyle/stringtype
                default: '3'
                options:
                - {label: Top (1), value: '1'}
                - {label: Bottom (2), value: '2'}
                - {label: Both (3), value: '3'}
    - !mobyle/inputprogramparagraph
        prompt: Output options
        name: output_opt
        argpos: 10
        children:
        - !mobyle/inputprogramparameter
            prompt: Output format (-D)
            format: ( "" , " -D " + str( value ) )[ value is not None and value !=
                vdef]
            name: outformat
            command: false
            type: !mobyle/stringtype
                default: '0'
                options:
                - {label: Traditional (0), value: '0'}
                - {label: Tabulated (1), value: '1'}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"bl2seq.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"bl2seq.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0493']
topics: ['EDAM_topic:0182']
env: {}