AbPrimerFinder_1.0.yaml

!mobyle/program
name: AbPrimerFinder
version: '1.0'
title: AbPrimerFinder
description: Identifies the forward and reverse primer of a sequence
authors: Kathy Yu,Yves Fomekong Nanfack
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter
        prompt: list of protein sequences in  (-A)
        format: '" " + str( value )'
        simple: true
        argpos: 20
        mandatory: true
        name: aafile
        command: false
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:2200']
            data_terms: ['EDAM_data:2044']
    - !mobyle/inputprogramparameter
        prompt: list of nucleotide sequences (-N)
        format: '"  " + str( value )'
        simple: true
        argpos: 30
        mandatory: true
        name: ntfile
        command: false
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:2200']
            data_terms: ['EDAM_data:2044']
    - !mobyle/inputprogramparameter
        comment: Heavy or Light chain sequences
        prompt: Heavy or Light chain sequences (-T)
        format: '"  " + str( value )'
        simple: true
        argpos: 10
        mandatory: true
        name: vType
        command: false
        type: !mobyle/stringtype
            default: VH
            options:
            - {label: VH, value: VH}
            - {label: VL, value: VL}
    - !mobyle/inputprogramparameter {comment: "The excel file has to be organized\
            \ as follow- One  sheet for VH FORWARD, VH REVERSE, VL FORWARD, VL REVERSE.-\
            \ Each sheet has 3 columns as PRIMERNAME\tAA\tNT , where AA and NT are\
            \ respectively the amino acids and the nucleotides sequence.", prompt: excel
            file with the list of primers  (-P), format: '("", "  " + str(value))[value
            is not None]', simple: true, argpos: 40, mandatory: true, name: parameterPrimerFile,
        command: false}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparagraph
        prompt: Output parameters
        name: outputparam
        argpos: 5
        children:
        - !mobyle/outputprogramparameter
            prompt: PRIMER LIST.
            filenames: '"*.out"'
            name: results
            output_type: stdout
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2048']
        - !mobyle/outputprogramparameter {comment: analysis, prompt: NEW PRIMER, filenames: '"*.csv"',
            name: dat}
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"AbPrimerFinder.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
comment: "As input, the program  reads a list of protein sequences and their corresponding\
    \ NT sequences, both in fasta format. In addition, the program reads an excel\
    \ file containing a list of predefined primers.\n                \tEach sequence\
    \ should be a variable domain. The AA sequence should be from FR1 to FR4. 3 cases\
    \ scenario are possible:- Perfect match: an existing primer is idenfied (AA match\
    \ and NT match).                     e.g: DA0000004881_a03 \tForward:\tMSVH3_f1_NcoI\t\
    AA:\tEVQLV \tNT:\tGaGgtgcagctggtg\t;- Half match:  an existing primer is identified\
    \ at the AA level, but the NT sequence is new. e.g: DA0000004881_a03 Reverse:\t\
    Rev_VH1\tAA:\tVTVSS\tNEW NT:\tGTCACCGTCTCTTCG- No match, none of the existing\
    \ AA primers could be identified;                             e.g: DA0000004881_a01\
    \ \tForward:\tNEW PRIMER\tAA:\t    \tNT:\tNEWIf any new primer is identified,\
    \ a excel file (in csv format) is returned additionaly."
operations: ['EDAM_operation:0308']
topics: ['EDAM_topic:0632']
command: source /sgcomp/aletheia/etc/aletheia_YFNconfig.bash; source /sgcomp/aletheia/packages/x86_64/Matlab/Config/.linux2013a.bashrc;
    /sgcomp/aletheia/packages/x86_64/Matlab/Documents/Projects/Bin/PrimerFinder/PrimerFinder/src/run_PrimerFinder.sh  $MCR_ROOT
env: {}