#@UGENE_WORKFLOW
#This schema allows to analyze sequence with Query and save results as alignment of selected features.
#To execute the workflow do the following:
#1) Select "Sequence Reader" task and specify source file at "URL" field in the Property Editor.
#2) Select "Annotate with UQL" task and specify the URL of the UQL schema file.
#3) Select "Filter annotations by name" task and specify the name of features to be joined into alignment.
#4) Select "Join sequences into alignment" task and specify the URL of the result file.
#

workflow "Convert UQL schema results to alignment" {
    read-sequence {
        type:read-sequence;
        name:"Read sequence";
        merge-gap:10;
        mode:0;
    }
    query {
        type:query;
        name:"Annotate with UQL";
        merge:false;
        offset:0;
    }
    extract-annotated-sequence {
        type:extract-annotated-sequence;
        name:"Get sequences by annotations";
        complement:true;
        extend-left:0;
        extend-right:0;
        merge-gap-length:1;
        translate:false;
    }
    sequences-to-msa {
        type:sequences-to-msa;
        name:"Join sequences into alignment";
    }
    write-msa {
        type:write-msa;
        name:"Write alignment";
        document-format:clustal;
        write-mode:2;
        url-out:output.aln;
    }
    filter-annotations {
        type:filter-annotations;
        name:"Filter annotations by name";
        accept-or-filter:true;
    }

    read-sequence.sequence->query.in-sequence.sequence
    filter-annotations.annotations->extract-annotated-sequence.in-sequence.annotations
    read-sequence.sequence->extract-annotated-sequence.in-sequence.sequence
    extract-annotated-sequence.sequence->sequences-to-msa.in-sequence.sequence
    sequences-to-msa.msa->write-msa.in-msa.msa
    query.annotations->filter-annotations.in-annotations.annotations

    .meta {
        visual {
            read-sequence {
                pos:"-765 -795";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-sequence.angle:360;
            }
            query {
                pos:"-615 -795";
                style:ext;
                bg-color-ext:"0 128 128 64";
                bounds:"-30 -30 75 91";
                in-sequence.angle:180;
                out-annotations.angle:360;
            }
            read-sequence.out-sequence->query.in-sequence {
                text-pos:"-27.5 -24";
            }
            extract-annotated-sequence {
                pos:"-255 -795";
                style:ext;
                bg-color-ext:"0 128 128 64";
                bounds:"-30 -30 116 105";
                in-sequence.angle:183.18;
                out-sequence.angle:294.642;
            }
            sequences-to-msa {
                pos:"-255 -585";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-sequence.angle:45;
                out-msa.angle:291.49;
            }
            extract-annotated-sequence.out-sequence->sequences-to-msa.in-sequence {
                text-pos:"-45 -37";
            }
            write-msa {
                pos:"-240 -390";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-msa.angle:73.0725;
            }
            sequences-to-msa.out-msa->write-msa.in-msa {
                text-pos:"-43.5 -24";
            }
            filter-annotations {
                pos:"-475 -795";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-annotations.angle:180;
                out-annotations.angle:360;
            }
            query.out-annotations->filter-annotations.in-annotations {
                text-pos:"-45 -37";
            }
            filter-annotations.out-annotations->extract-annotated-sequence.in-sequence {
                text-pos:"-45 -37";
            }
        }
        wizard {
            name:"Convert UQL schema results to alignment Wizard";
            help-page-id:16122706;
            page {
                id:1;
                next:2;
                title:"Input sequence(s)";
                parameters-area {
                    read-sequence.url-in {
                        type:datasets;
                    }
                }
            }
            page {
                id:2;
                title:"Annotate with UQL";
                parameters-area {
                    group {
                        title:"UQL parameters";
                        label-size:120;
                        query.url-in {
                            label:"UQL schema file";
                        }
                        query.merge {
                        }
                        query.offset {
                        }
                    }
                    group {
                        title:"Filter annotations parameters";
                        label-size:120;
                        filter-annotations.annotation-names {
                        }
                        filter-annotations.accept-or-filter {
                        }
                    }
                    group {
                        title:"Output data";
                        label-size:120;
                        write-msa.url-out {
                            label:"Result file";
                        }
                        write-msa.document-format {
                        }
                    }
                }
            }
        }
    }
}