#@UGENE_WORKFLOW
#Build frequency matrix from existing multiple sequence alignment



workflow "Build frequency matrix"{

    read-msa {
        type:read-msa;
        name:"Read alignment";
        url-in {
            dataset:"Dataset 1";
        }
    }
    fmatrix-build {
        type:fmatrix-build;
        name:"Build frequency matrix";
    }
    fmatrix-write {
        type:fmatrix-write;
        name:"Write frequency matrix";
    }


    .actor-bindings {
        read-msa.out-msa->fmatrix-build.in-msa
        fmatrix-build.out-fmatrix->fmatrix-write.in-fmatrix
    }

    read-msa.msa->fmatrix-build.in-msa.msa
    fmatrix-build.fmatrix->fmatrix-write.in-fmatrix.fmatrix

    .meta {
        parameter-aliases {
            read-msa.url-in {
                alias:in;
                description:"Input alignment";
            }
            fmatrix-build.matrix-type {
                alias:type;
                description:"Frequency matrix type (using 'Mononucleic' by default)";
            }
            fmatrix-write.url-out {
                alias:out;
                description:"Output frequency matrix";
            }
        }
        visual {
            fmatrix-build {
                pos:"-600 -645";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-msa.angle:180;
                out-fmatrix.angle:360;
            }
            fmatrix-write {
                pos:"-390 -645";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-fmatrix.angle:180;
            }
            read-msa {
                pos:"-780 -645";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-msa.angle:360;
            }
            fmatrix-build.out-fmatrix->fmatrix-write.in-fmatrix {
                text-pos:"-45 -37";
            }
            read-msa.out-msa->fmatrix-build.in-msa {
                text-pos:"-45 -50";
            }
        }
    }
}