#@UGENE_WORKFLOW
#For each input multiple alignment the workflow calculates the consensus and saves it to a text file, named according to the name of the input alignment.
#
#The JalView algorithm (denoted as "default") is used by default to calculate the consensus. For each column of the alignment it returns either "+", if there are 2 characters with high frequency in this column, or a character in uppercase or lowercase. The case of the character depends on the percentage value of the character in the column and the "threshold" value.
#
#Alternatively, you can use the ClustalW algorithm to calculate the consensus:
# - If all characters in a column are exactly the same, the algorithm sets asterisk value ("*") to the corresponding position of the consensus.
# - A colon value (":") indicates conservation between groups of strongly similar properties, i.e. the scoring value is greater than 0.5 in the Gonnet PAM 250 matrix (see documentation for details).
# - If the scoring value is less than 0.5, the period (".") value is inserted.
# - Otherwise, the algorithm inserts space (" ").
#The "threshold" parameter is not applied to this algorithm.

workflow "Extract consensus as text"{

    read-msa {
        type:read-msa;
        name:"Read Alignment";
        url-in {
            dataset:"Dataset 1";
        }
    }
    write-text {
        type:write-text;
        name:"Write Plain Text";
        url-out {
var re = /[\\\/]/;
var tokens = url.toString().split(re);
var dir = "";
if (tokens.length > 0) {
    dir = tokens[tokens.length-1];
}
url_out = dir + "_consensus.txt"
        };
        write-mode:0;
    }
    extract-msa-consensus-string {
        type:extract-msa-consensus-string;
        name:"Extract Consensus from Alignment as Text";
        algorithm:Clustal;
    }

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

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

    .meta {
        parameter-aliases {
            read-msa.url-in {
                alias:in;
            }
            extract-msa-consensus-string.algorithm {
                alias:algorithm;
            }
            extract-msa-consensus-string.threshold {
                alias:threshold;
            }
        }
        visual {
            extract-msa-consensus-string {
                pos:"-480 -600";
                style:ext;
                bg-color-ext:"0 128 0 64";
                in-msa.angle:180;
                out-text.angle:360;
            }
            read-msa {
                pos:"-720 -600";
                style:ext;
                bg-color-ext:"24 102 175 64";
                bounds:"-30 -30 68.25 69";
                out-msa.angle:360;
            }
            write-text {
                pos:"-165 -600";
                style:ext;
                bg-color-ext:"64 26 96 64";
                bounds:"-30 -30 102 73";
                in-text.angle:180;
            }
            extract-msa-consensus-string.out-text->write-text.in-text {
                text-pos:"-30 -24";
            }
            read-msa.out-msa->extract-msa-consensus-string.in-msa {
                text-pos:"-45 -50";
            }
        }
        wizard {
            name:"Extract Alignment Consensus as Text";
            help-page-id:16122702;
            auto-run: true;
            page {
                id:1;
                next:2;
                title:"Input Multiple Alighments";
                parameters-area {
                    read-msa.url-in {
                        type:datasets;
                    }
                }
            }
            page {
                id:2;
                next:3;
                title:"Extracting Consensus Settings";
                parameters-area {
                    group {
                        title:"Extracting Consensus as Text Worker Settings";
                        label-size:120;
                        extract-msa-consensus-string.algorithm {
                        }
                        extract-msa-consensus-string.threshold {
                        }
                    }
                }
            }
            page {
                id:3;
                title:"Output Files";
                parameters-area {
                    label {
                        text:"For each input alignment the workflow outputs separate text file with consensus in it.";
                        background-color:rgb(203,222,228);
                    }
                }
            }
        }
    }
}