blast2mydb.yaml

!mobyle/program
name: blast2mydb
title: BLAST2MYDB
description: NCBI BLAST, with gaps against my sequences database
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparagraph
        prompt: Create my Database
        name: db
        children:
        - !mobyle/inputprogramparameter
            format: '"formatdb "'
            argpos: 1
            name: formatdb
            command: false
            hidden: true
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            comment: Create a protein database for blastx
            prompt: Protein db
            format: '" -i "+ str(value)'
            simple: true
            argpos: 2
            mandatory: true
            name: protein_db
            precond:
                blast2:
                    '#in': [blastx, blastp]
            command: false
            type: !mobyle/formattedtype
                format_terms: ['EDAM_format:2200']
                data_terms: ['EDAM_data:2044']
        - !mobyle/inputprogramparameter
            comment: Create a nucleotid database for blastn, tblastn or tblastx
            prompt: Nucleotid db
            format: '"-p F -i "+ str(value)'
            simple: true
            argpos: 2
            mandatory: true
            name: nucleotid_db
            precond:
                blast2:
                    '#in': [blastn, tblastx, tblastn, psitblastn]
            command: false
            type: !mobyle/formattedtype
                format_terms: ['EDAM_format:2200']
                data_terms: ['EDAM_data:2044']
        - !mobyle/inputprogramparameter
            prompt: the name of my db
            format: '" -n " + str( value )'
            simple: true
            argpos: 3
            mandatory: true
            name: db_name
            command: false
            type: !mobyle/stringtype {default: myDatabase}
    - !mobyle/inputprogramparameter
        prompt: Blast initiation
        format: '" && blastall "'
        argpos: 4
        name: blast_init
        command: true
        hidden: true
        type: !mobyle/stringtype {}
    - !mobyle/inputprogramparameter
        comment: '- Blastp compares an amino acid query sequence against a protein
            sequence database;- Blastn compares a nucleotide query sequence against
            a nucleotide sequence database;- Blastx compares the six-frame conceptual
            translation products of a nucleotide query sequence (both strands) against
            a protein sequence database;- tBlastn compares a protein query sequence
            against a nucleotide sequence database dynamically translated in all six
            reading frames (both strands).- tBlastx compares the six-frame translations
            of a nucleotide query sequence against the six-frame translations of a
            nucleotide sequence database.- psitBlastn compares a protein query sequence
            against a nucleotide sequence database dynamically translated in all six
            reading frames (both strands) using a position specific matrix created
            by PSI-BLAST.'
        prompt: Blast program (-p)
        format: '" -p "+ str(value)'
        simple: true
        argpos: 5
        mandatory: true
        name: blast2
        command: false
        type: !mobyle/stringtype
            default: 'null'
            options:
            - {label: Choose a program, value: 'null'}
            - {label: Blastn (nucleotide query / nucleotide db), value: blastn}
            - {label: Blastx (translated nucleotide query / protein db), value: blastx}
            - {label: tBlastx (translated nucleotide query / translated nucleotide
                    db), value: tblastx}
            - {label: Blastp (protein query / protein db), value: blastp}
            - {label: tBlastn (protein query / translated nucleotide db), value: tblastn}
            - {label: psitBlastn (protein query / translated nucleotide db), value: psitblastn}
    - !mobyle/inputprogramparameter
        format: '" -d "+ str( db_name )'
        argpos: 6
        name: blastdb
        command: false
        hidden: true
        type: !mobyle/stringtype {}
    - !mobyle/inputprogramparagraph
        prompt: Query Sequence
        name: query
        argpos: 10
        children:
        - !mobyle/inputprogramparameter
            comment: Read (first, query) sequence or set from file
            prompt: Query (-i)
            format: '" -i "+ str(query_seq)'
            simple: true
            mandatory: true
            name: query_seq
            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 query sequence (-L)
            name: start_region
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            comment: Location on query sequence
            prompt: End of required region in query sequence (-L)
            format: (' -L "%s"' % (str(start_region)), ' -L "%s %s"' % (str(start_region),
                str(value)))[value is not None]
            name: end_region
            precond:
                start_region: {'#ne': None}
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            prompt: Number of concatenated queries (blastn or tblastn) (-B)
            format: ("" , " -B "+str(value))[value is not None]
            name: concat
            precond:
                blast2:
                    '#in': [blastn, tblastn]
            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 tblastn'
            prompt: Cost to open a gap (-G)
            format: ("" , " -G "+str(value))[value is not None]
            name: open_a_gap
            command: false
            type: !mobyle/floattype {}
        - !mobyle/inputprogramparameter
            comment: 'Default: 2 for blastn; 1 for blastp, blastx and tblastnLimited
                values for gap existence and extension are supported for these programs.
                Some supported and suggested values are:Existence Extension10 -- 110
                -- 211 -- 18 -- 29 -- 2'
            prompt: Cost to extend a gap (-E)
            format: ("" , " -E "+str(value))[value is not None]
            name: extend_a_gap
            command: false
            type: !mobyle/floattype {}
        - !mobyle/inputprogramparagraph
            prompt: Protein penalty (not for blastn)
            name: scoring_blast
            precond:
                blast2: {'#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: BLOSUM62, value: BLOSUM62}
                    - {label: BLOSUM45, value: BLOSUM45}
                    - {label: BLOSUM80, value: BLOSUM80}
                    - {label: PAM30, value: PAM30}
                    - {label: PAM70, value: PAM70}
        - !mobyle/inputprogramparagraph
            prompt: Blastn penalty
            name: scoring_blastn
            precond: {blast2: 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/floattype {default: -3.0}
            - !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/floattype {default: 1.0}
        - !mobyle/inputprogramparameter
            prompt: Frame shift penalty (-w)
            format: ("", " -w "+str(value))[value is not None]
            name: frameshift
            command: false
            type: !mobyle/floattype {}
    - !mobyle/inputprogramparagraph
        comment: BLAST 2.0 uses the dust low-complexity filter for blastn and seg
            for the other programs.If one uses '-F T' then normal filtering by seg
            or dust (for blastn) occurs (likewise '-F F' means no filtering whatsoever).
        prompt: Filtering and masking options
        name: filter_opt
        argpos: 20
        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
                - {'#not': other_masking}
            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
                - {'#not': other_filters}
            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")[ bool(value) ]
            name: lower_case
            command: false
            type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparagraph
        comment: The programs blastn and blastp offer fully gapped alignments. blastx
            and tblastn have 'in-frame' gapped alignments and use sum statistics to
            link alignments from different frames. tblastx provides only ungapped
            alignments.
        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: 'Default: zero for all programs'
            prompt: Multiple Hits window size (-A)
            format: ("" , " -A "+str(value))[value is not None]
            name: dist_hits
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            comment: Blast seeks first short word pairs whose aligned score reaches
                at least this value.Default values:- 0 for blastn- 11 for blastp-
                12 for blastx- 13 for tblastn and tblastx
            prompt: Threshold for extending hits (-f)
            format: ("" , " -f "+str(value))[value is not None]
            name: extend_hit
            command: false
            type: !mobyle/floattype {}
        - !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: Default values:- 50 for blastn- 0 for tblastx- 25 for others
            prompt: X dropoff value for final alignment gapped alignment (-Z)
            format: ("" , " -Z "+str(value))[value is not None]
            name: dropoff_final
            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
            comment: If this option is used, a value of 100 is recommended.
            prompt: Number of best hits from a region to keep (-K)
            format: ("" , " -K "+str(value))[value is not None]
            name: keep_hits
            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:
                blast2: {'#ne': tblastx}
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Single-hit or multiple-hit mode (-P)
            format: ("" , " -P "+str(value))[value != "0"]
            name: mode
            precond:
                blast2: {'#ne': blastn}
            command: false
            type: !mobyle/stringtype
                default: '0'
                options:
                - {label: Multiple-hit (0), value: '0'}
                - {label: Single-hit (1), value: '1'}
    - !mobyle/inputprogramparagraph
        prompt: Translation options
        name: translation_opt
        argpos: 30
        children:
        - !mobyle/inputprogramparameter
            prompt: Genetic code used for query translation (-Q)
            format: ("" , " -Q "+str(value))[value is not None and value != vdef]
            name: gc_query
            precond:
                blast2:
                    '#in': [blastx, tblastx]
            command: false
            type: !mobyle/stringtype
                default: '1'
                options:
                - {label: Standard (1), value: '1'}
                - {label: Vertebrate Mitochondrial (2), value: '2'}
                - {label: Yeast Mitochondrial (3), value: '3'}
                - {label: 'Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
                        (4)', value: '4'}
                - {label: Invertebrate Mitochondrial (5), value: '5'}
                - {label: Ciliate Macronuclear and Dasycladacean (6), value: '6'}
                - {label: Echinoderm Mitochondrial (9), value: '9'}
                - {label: Euplotid Nuclear (10), value: '10'}
                - {label: Bacterial (11), value: '11'}
                - {label: Alternative Yeast Nuclear (12), value: '12'}
                - {label: Ascidian Mitochondrial (13), value: '13'}
                - {label: Flatworm Mitochondrial (14), value: '14'}
                - {label: Blepharisma Macronuclear (15), value: '15'}
        - !mobyle/inputprogramparameter
            prompt: Genetic code used for database translation (-D)
            format: ("" , " -D "+str(value))[value != vdef]
            name: gc_db
            precond:
                blast2:
                    '#in': [tblastn, tblastx]
            command: false
            type: !mobyle/stringtype
                default: '1'
                options:
                - {label: Standard (1), value: '1'}
                - {label: Vertebrate Mitochondrial (2), value: '2'}
                - {label: Yeast Mitochondrial (3), value: '3'}
                - {label: 'Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
                        (4)', value: '4'}
                - {label: Invertebrate Mitochondrial (5), value: '5'}
                - {label: Ciliate Macronuclear and Dasycladacean (6), value: '6'}
                - {label: Echinoderm Mitochondrial (9), value: '9'}
                - {label: Euplotid Nuclear (10), value: '10'}
                - {label: Bacterial (11), value: '11'}
                - {label: Alternative Yeast Nuclear (12), value: '12'}
                - {label: Ascidian Mitochondrial (13), value: '13'}
                - {label: Flatworm Mitochondrial (14), value: '14'}
                - {label: Blepharisma Macronuclear (15), value: '15'}
        - !mobyle/inputprogramparameter
            prompt: Query strands to search against database (-S)
            format: ("" , " -S "+str(value))[value is not None and value != vdef]
            name: strand
            precond:
                blast2:
                    '#in': [blastn, blastx, tblastx]
            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: Report options
        name: affichage
        argpos: 40
        children:
        - !mobyle/inputprogramparameter
            comment: Maximum number of database sequences for which one-line descriptions
                will be reported.
            prompt: Number of one-line descriptions to show (-v)
            format: ("" , " -v "+str(value))[value is not None and value != vdef]
            name: Descriptions
            command: false
            type: !mobyle/integertype {default: 500}
        - !mobyle/inputprogramparameter
            comment: Maximum number of database sequences for which high-scoring segment
                pairs will be reported (-b).
            prompt: Number of database sequences to show alignments (-b)
            format: ("" , " -b "+str(value))[value is not None and value != vdef]
            name: Alignments
            command: false
            type: !mobyle/integertype {default: 250}
        - !mobyle/inputprogramparameter
            prompt: Alignment view options (-m)
            format: ("" , " -m "+str(value))[value is not None and value != vdef]
            name: view_alignments
            command: false
            type: !mobyle/stringtype
                default: '0'
                options:
                - {label: Pairwise (0), value: '0'}
                - {label: Query-anchored showing identities (1), value: '1'}
                - {label: Query-anchored no identities (2), value: '2'}
                - {label: 'Flat query-anchored, show identities (3)', value: '3'}
                - {label: 'Flat query-anchored, no identities (5)', value: '4'}
                - {label: Query-anchored no identities and blunt ends (5), value: '5'}
                - {label: 'Flat query-anchored, no identities and blunt ends (6)',
                    value: '6'}
                - {label: XML Blast output (7), value: '7'}
                - {label: Tabular output (8), value: '8'}
        - !mobyle/inputprogramparameter
            prompt: Text output file
            format: '" -o blast2.txt"'
            argpos: 50
            name: txtoutput
            precond:
                view_alignments: {'#ne': '7'}
            command: false
            hidden: true
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            prompt: Xml output file
            format: '" -o blast2.xml"'
            argpos: 60
            name: xmloutput
            precond: {view_alignments: '7'}
            command: false
            hidden: true
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            prompt: Html output
            format: ("" , " && html4blast -g -o blast2.html blast2.txt")[value]
            argpos: 61
            name: htmloutput
            precond:
                view_alignments:
                    '#nin': ['7', '8']
            command: false
            type: !mobyle/booleantype {default: false}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter
        prompt: Blast text report
        filenames: '"blast2.txt"'
        name: txtfile
        precond:
            view_alignments: {'#ne': '7'}
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:0857']
    - !mobyle/outputprogramparameter
        prompt: Blast xml report
        filenames: '"blast2.xml"'
        name: xmlfile
        precond: {view_alignments: '7'}
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Blast html report
        filenames: '"blast2.html"'
        name: htmlfile
        precond:
            view_alignments:
                '#nin': ['7', '8']
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        filenames: '"*.gif"'
        name: imgfile
        precond:
            view_alignments:
                '#nin': ['7', '8']
        hidden: true
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"blast2mydb.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"blast2mydb.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0352', 'EDAM_operation:0227']
topics: ['EDAM_topic:0182', 'EDAM_topic:0220']
references:
- {doi: null, label: 'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaeffer,Jinghui
        Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), Gapped BLAST
        and PSI-BLAST: a new generation of protein database search programs, Nucleic
        Acids Res. 25:3389-3402.', url: null}
documentation_links: ['http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=handbook.chapter.ch16',
    'http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/tut1.html']
env: {}