#@UGENE_WORKFLOW
#Performs multiple sequence alignment with MUSCLE algorithm and saves the resulting alignment to file. Source data can be of any format containing sequences or alignments.
#



workflow align{

    read-msa {
        type:read-msa;
        name:"Read alignment";
        url-in {
            dataset:"Dataset 1";
        }
    }
    muscle {
        type:muscle;
        name:"Align with MUSCLE";
    }
    write-msa {
        type:write-msa;
        name:"Write alignment";
        write-mode:1;
    }


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

    read-msa.msa->muscle.in-msa.msa
    muscle.msa->write-msa.in-msa.msa

    .meta {
        parameter-aliases {
            read-msa.url-in {
                alias:in;
                description:"Input alignment";
            }
            muscle.max-iterations {
                alias:max-iterations;
                description:"Maximum number of iterations (using '2' by default)";
            }
            muscle.mode {
                alias:mode;
                description:"Selector of preset configurations, that give you the choice of optimizing accuracy, speed,or some compromise between the two. The default favors accuracy (using 'MUSCLE default' by default)";
            }
            muscle.range {
                alias:range;
                description:"Whole alignment or column range e.g. 1..100 (using 'Whole alignment' by default)";
            }
            muscle.stable {
                alias:stable;
                description:"Do not rearrange aligned sequences (using 'True' by default)";
            }
            write-msa.document-format {
                alias:format;
                description:"Document format of output alignment (using 'clustal' by default)";
            }
            write-msa.url-out {
                alias:out;
                description:"Output alignment";
            }
        }
        visual {
            muscle {
                pos:"-570 -645";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-msa.angle:180;
                out-msa.angle:360;
            }
            read-msa {
                pos:"-765 -645";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-msa.angle:360;
            }
            write-msa {
                pos:"-330 -645";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-msa.angle:180;
            }
            muscle.out-msa->write-msa.in-msa {
                text-pos:"-45 -50";
            }
            read-msa.out-msa->muscle.in-msa {
                text-pos:"-45 -50";
            }
        }
    }
}