#@UGENE_WORKFLOW
#Uses input assemblies to extract the consensus sequences and save them to a FASTA.



workflow "Extract consensus from assembly"{

    read-assembly {
        type:read-assembly;
        name:"Read Assembly";
        url-in {
            dataset:"Dataset 1";
        }
    }
    write-sequence {
        type:write-sequence;
        name:"Write Sequence";
        url-out:consensus.fa;
    }
    extract-consensus {
        type:extract-consensus;
        name:"Extract Consensus from Assembly";
    }

    .actor-bindings {
        extract-consensus.out-sequence->write-sequence.in-sequence
        read-assembly.out-assembly->extract-consensus.in-assembly
    }

    extract-consensus.sequence->write-sequence.in-sequence.sequence
    read-assembly.assembly->extract-consensus.in-assembly.assembly

    .meta {
        parameter-aliases {
            read-assembly.url-in {
                alias:in;
            }
            write-sequence.url-out {
                alias:out;
            }
            extract-consensus.algorithm {
                alias:algo;
            }
            extract-consensus.keep-gaps {
                alias:gaps;
            }
        }
        visual {
            extract-consensus {
                pos:"-645 -585";
                style:ext;
                bg-color-ext:"0 129 94 64";
                in-assembly.angle:180;
                out-sequence.angle:360;
            }
            read-assembly {
                pos:"-840 -585";
                style:ext;
                bg-color-ext:"24 102 175 64";
                out-assembly.angle:360;
            }
            write-sequence {
                pos:"-360 -585";
                style:ext;
                bg-color-ext:"64 26 96 64";
                in-sequence.angle:180;
            }
            extract-consensus.out-sequence->write-sequence.in-sequence {
                text-pos:"-37 -24";
            }
            read-assembly.out-assembly->extract-consensus.in-assembly {
                text-pos:"-26.5 -24";
            }
        }
        wizard {
            name:"Extract Consensus Wizard";
            help-page-id:16122723;
            page {
                id:1;
                title:"Extract Consensus";
                parameters-area {
                    group {
                        title:"Input parameters";
                        label-size:120;
                        read-assembly.url-in {
                            label:Assembly;
                        }
                        extract-consensus.algorithm {
                            label:Algorithm;
                        }
                        extract-consensus.keep-gaps {
                            label:"Keep gaps";
                        }
                    }
                    group {
                        title:"Extracted consensus";
                        label-size:120;
                        write-sequence.url-out {
                            label:"Output file";
                        }
                    }
                }
            }
        }
    }
}