#@UGENE_WORKFLOW
#This workflows allows one to extract a consensus as a text. In inputs a number of alignments and for each of them outputs consensus as a text. The consensus sequence is calculated according to the algorithm selected



workflow "New workflow"{

    read-msa {
        type:read-msa;
        name:"Read Alignment";
        url-in {
            dataset:"Dataset 1";
        }
    }
    extract-msa-consensus-string {
        type:extract-msa-consensus-string;
        name:"Extract Consensus from Alignment as String";
    }
    write-text {
        type:write-text;
        name:"Write Plain Text";
        write-mode:0;
    }

    .actor-bindings {
        extract-msa-consensus-string.out-text->write-text.in-text
        read-msa.out-msa->extract-msa-consensus-string.in-msa
    }

    read-msa.msa->extract-msa-consensus-string.in-msa.msa
    extract-msa-consensus-string.text->write-text.in-text.text

    .meta {
        parameter-aliases {
            read-msa.url-in {
                alias:in;
            }
            extract-msa-consensus-string.algorithm {
                alias:algorithm;
            }
            extract-msa-consensus-string.threshold {
                alias:threshold;
            }
            write-text.data-storage {
                alias:storage;
            }
            write-text.database {
                alias:db;
            }
            write-text.db-path {
                alias:out_path;
            }
            write-text.url-out {
                alias:out;
            }
        }
        visual {
            extract-msa-consensus-string {
                pos:"-495 -570";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-msa.angle:180;
                out-text.angle:360;
            }
            read-msa {
                pos:"-645 -570";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-msa.angle:360;
            }
            write-text {
                pos:"-240 -570";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-text.angle:180;
            }
            extract-msa-consensus-string.out-text->write-text.in-text {
                text-pos:"-24 -24";
            }
            read-msa.out-msa->extract-msa-consensus-string.in-msa {
                text-pos:"-45 -50";
            }
        }
    }
}