#@UGENE_WORKFLOW
#This workflows allows one to extract a consensus sequence. In inputs a number of alignments and for each of them outputs consensus as a sequence. 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";
        }
    }
    write-sequence {
        type:write-sequence;
        name:"Write Sequence";
        write-mode:0;
    }
    extract-msa-consensus-sequence {
        type:extract-msa-consensus-sequence;
        name:"Extract Consensus from Alignment as Sequence";
    }

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

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

    .meta {
        parameter-aliases {
            read-msa.url-in {
                alias:in;
            }
            write-sequence.data-storage {
                alias:storage;
            }
            write-sequence.database {
                alias:db;
            }
            write-sequence.db-path {
                alias:out_path;
            }
            write-sequence.document-format {
                alias:format;
            }
            write-sequence.url-out {
                alias:out;
            }
            extract-msa-consensus-sequence.algorithm {
                alias:algorithm;
            }
            extract-msa-consensus-sequence.keep-gaps {
                alias:keep_gaps;
            }
            extract-msa-consensus-sequence.threshold {
                alias:threshold;
            }
        }
        visual {
            extract-msa-consensus-sequence {
                pos:"-525 -615";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-msa.angle:180;
                out-sequence.angle:360;
            }
            read-msa {
                pos:"-690 -615";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-msa.angle:360;
            }
            write-sequence {
                pos:"-285 -615";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-sequence.angle:180;
            }
            extract-msa-consensus-sequence.out-sequence->write-sequence.in-sequence {
                text-pos:"-37 -24";
            }
            read-msa.out-msa->extract-msa-consensus-sequence.in-msa {
                text-pos:"-45 -50";
            }
        }
    }
}