#@UGENE_WORKFLOW
# The workflow takes two sets of annotations as input (denoted as A and B).
# It intersects the sets and outputs the result annotations.
#
#There are three options for the output:
#   - Shared intervals between overlapped annotations from A and B;
#   - Annotations from A that overlap annotations from B;
#   - Annotations from A that DO NOT overlap annotations from B.
#
#It is also possible to tweak the percentage of the minimum overlap between A and B annotations.



workflow "Intersect annotations"{

    intersect-annotations {
        type:intersect-annotations;
        name:"Intersect Annotations";
    }
    read-annotations {
        type:read-annotations;
        name:"Read Annotations A";
        url-in {
            dataset:"Dataset 1";
        }
    }
    read-annotations-1 {
        type:read-annotations;
        name:"Read Annotations B";
        url-in {
            dataset:"Dataset 1";
        }
    }
    write-annotations {
        type:write-annotations;
        name:"Write Annotations";
        url-out:intersect.gb;
    }

    .actor-bindings {
        intersect-annotations.output-intersect-annotations->write-annotations.in-annotations
        read-annotations-1.out-annotations->intersect-annotations.input-annotations-b
        read-annotations.out-annotations->intersect-annotations.input-annotations-a
    }

    read-annotations.annotations->intersect-annotations.input-annotations-a.input-annotations-a
    read-annotations-1.annotations->intersect-annotations.input-annotations-b.input-annotations-b
    intersect-annotations.output-intersect-annotations->write-annotations.in-annotations.annotations
    read-annotations-1.annotations->write-annotations.in-annotations.annotations
    read-annotations.annotations->write-annotations.in-annotations.annotations

    .meta {
        parameter-aliases {
            intersect-annotations.minimum-overlap {
                alias:min-overlap;
            }
            intersect-annotations.report {
                alias:report;
            }
            intersect-annotations.unique {
                alias:unique;
            }
            read-annotations.url-in {
                alias:in-A;
            }
            read-annotations-1.url-in {
                alias:in-B;
            }
            write-annotations.document-format {
                alias:out-format;
            }
            write-annotations.url-out {
                alias:out-file;
            }
        }
        visual {
            intersect-annotations {
                pos:"-477 -583";
                style:ext;
                bg-color-ext:"207 74 41 64";
                input-annotations-a.angle:150;
                input-annotations-b.angle:210;
                output-intersect-annotations.angle:360;
            }
            read-annotations {
                pos:"-810 -693";
                style:ext;
                bg-color-ext:"0 141 212 64";
                bounds:"-30 -30 148.875 87";
                out-annotations.angle:360;
            }
            read-annotations-1 {
                pos:"-813 -485";
                style:ext;
                bg-color-ext:"0 141 212 64";
                bounds:"-30 -30 157.5 82";
                out-annotations.angle:360;
            }
            write-annotations {
                pos:"-122 -583";
                style:ext;
                bg-color-ext:"117 86 175 64";
                in-annotations.angle:180;
            }
            intersect-annotations.output-intersect-annotations->write-annotations.in-annotations {
                text-pos:"-45 -62";
            }
            read-annotations-1.out-annotations->intersect-annotations.input-annotations-b {
                text-pos:"-44.9609 -28";
            }
            read-annotations.out-annotations->intersect-annotations.input-annotations-a {
                text-pos:"-44.9609 -28";
            }
        }
        wizard {
            name:"Intersect Annotations Wizard";
            help-page-id:16123490;
            auto-run: true;
            page {
                id:1;
                title:"Intersect annotations parameters";
                parameters-area {
                    group {
                        title:"Input data";
                        label-size:120;
                        read-annotations.url-in {
                            label:"Annotations A";
                        }
                        read-annotations-1.url-in {
                            label:"Annotations B";
                        }
                    }
                    group {
                        title:"Output data";
                        label-size:120;
                        intersect-annotations.report {
                            label:Report;
                        }
                        write-annotations.url-out {
                            label:"Output file";
                        }
                    }
                }
            }
        }
    }
}