#@UGENE_WORKFLOW
#For each input sequence the workflow performs a search of inverted repeats. Then it saves the repeats found on the direct strand to the "direct_strand_repeat_units.fa" file and the complement ones to the "compl_strand_repeat_units.fa" file.

include "Get the first half of sequence.usa" as "Script-Get the first half of sequence"
include "Get the second half of sequence.usa" as "Script-Get the second half of sequence"

workflow "Search for inverted repeats"{

    read-sequence {
        type:read-sequence;
        name:"Read Sequence";
        url-in {
            dataset:"Dataset 1";
        }
    }
    repeats-search {
        type:repeats-search;
        name:"Find Inverted Repeats";
        algorithm:0;
        exclude-tandems:false;
        filter-algorithm:0;
        identity:90;
        inverted:true;
        max-distance:5000;
        min-distance:100;
        min-length:10;
        threads:0;
    }
    extract-annotated-sequence {
        type:extract-annotated-sequence;
        name:"Get Sequences by Annotations";
    }
    reverse-complement {
        type:reverse-complement;
        name:"Reverse Complement";
    }
    write-sequence {
        type:write-sequence;
        name:"Write the Direct Strand Repeat Unit";
        url-out:direct_strand_repeat_units.fa;
    }
    write-sequence-1 {
        type:write-sequence;
        name:"Write the Direct Strand Repeat Unit";
        url-out:compl_strand_repeat_units.fa;
    }
    Script-Get-the-first-half-of-sequence {
        type:"Script-Get the first half of sequence";
        name:"Get the First Half of Sequence";
        script {
out_sequence = subsequence(in_sequence, 0, size(in_sequence) / 2 - 1);
        };
    }
    Script-Get-the-second-half-of-sequence {
        type:"Script-Get the second half of sequence";
        name:"Get the Second Half of Sequence";
        script {
out_sequence = subsequence(in_sequence, size(in_sequence) / 2, size(in_sequence) - 1);
        };
    }

    .actor-bindings {
        read-sequence.out-sequence->repeats-search.in-sequence
        repeats-search.out-annotations->extract-annotated-sequence.in-sequence
        extract-annotated-sequence.out-sequence->Script-Get-the-second-half-of-sequence.in
        extract-annotated-sequence.out-sequence->Script-Get-the-first-half-of-sequence.in
        reverse-complement.out-sequence->write-sequence-1.in-sequence
        Script-Get-the-first-half-of-sequence.out->write-sequence.in-sequence
        Script-Get-the-second-half-of-sequence.out->reverse-complement.in-sequence
    }

    read-sequence.sequence->repeats-search.in-sequence.sequence
    repeats-search.annotations->extract-annotated-sequence.in-sequence.annotations
    read-sequence.sequence->extract-annotated-sequence.in-sequence.sequence
    Script-Get-the-second-half-of-sequence.sequence->reverse-complement.in-sequence.sequence
    Script-Get-the-first-half-of-sequence.sequence->write-sequence.in-sequence.sequence
    reverse-complement.sequence->write-sequence-1.in-sequence.sequence
    extract-annotated-sequence.sequence->Script-Get-the-first-half-of-sequence.in.sequence
    extract-annotated-sequence.sequence->Script-Get-the-second-half-of-sequence.in.sequence

    .meta {
        visual {
            Script-Get-the-first-half-of-sequence {
                pos:"-491 -642";
                style:ext;
                bg-color-ext:"85 170 255 64";
                in.angle:58.5704;
                out.angle:290.298;
            }
            Script-Get-the-second-half-of-sequence {
                pos:"-217 -651";
                style:ext;
                bg-color-ext:"85 170 255 64";
                bounds:"-30 -30 81.625 81";
                in.angle:47.0454;
                out.angle:288.06;
            }
            extract-annotated-sequence {
                pos:"-386 -822";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-sequence.angle:180;
                out-sequence.angle:294.605;
            }
            read-sequence {
                pos:"-932 -828";
                style:ext;
                bg-color-ext:"255 170 127 64";
                out-sequence.angle:360;
            }
            repeats-search {
                pos:"-735 -828";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-sequence.angle:180;
                out-annotations.angle:358.946;
            }
            reverse-complement {
                pos:"-221 -487";
                style:ext;
                bg-color-ext:"0 128 128 64";
                bounds:"-30 -30 114.5 81";
                in-sequence.angle:44.1931;
                out-sequence.angle:292.714;
            }
            write-sequence {
                pos:"-486 -471";
                style:ext;
                bg-color-ext:"170 170 0 64";
                bounds:"-30 -30 87 112";
                in-sequence.angle:49.844;
            }
            write-sequence-1 {
                pos:"-209 -297";
                style:ext;
                bg-color-ext:"170 170 0 64";
                bounds:"-30 -30 97.25 102";
                in-sequence.angle:50.5275;
            }
            Script-Get-the-first-half-of-sequence.out->write-sequence.in-sequence {
                text-pos:"-30.5 -12";
            }
            Script-Get-the-second-half-of-sequence.out->reverse-complement.in-sequence {
                text-pos:"-32.5 -13";
            }
            extract-annotated-sequence.out-sequence->Script-Get-the-first-half-of-sequence.in {
                text-pos:"-38 -15";
            }
            extract-annotated-sequence.out-sequence->Script-Get-the-second-half-of-sequence.in {
                text-pos:"-52 -19";
            }
            read-sequence.out-sequence->repeats-search.in-sequence {
                text-pos:"-27.5 -24";
            }
            repeats-search.out-annotations->extract-annotated-sequence.in-sequence {
                text-pos:"-45 -37";
            }
            reverse-complement.out-sequence->write-sequence-1.in-sequence {
                text-pos:"-37 -21";
            }
        }
        wizard {
            name:"Search for Inverted Repeats Wizard";
            help-page-id:16122701;
            page {
                id:1;
                next:2;
                title:"Input sequence(s)";
                parameters-area {
                    read-sequence.url-in {
                        type:datasets;
                    }
                }
            }
            page {
                id:2;
                next:3;
                title:"Search for inverted repeats parameters";
                parameters-area {
                    group {
                        title:"Find Inverted Repeats parameters";
                        label-size:150;
                        repeats-search.result-name {
                        }
                        repeats-search.min-length {
                        }
                        repeats-search.identity {
                        }
                        repeats-search.min-distance {
                        }
                        repeats-search.max-distance {
                        }
                        repeats-search.filter-algorithm {
                        }
                        repeats-search.algorithm {
                        }
                        repeats-search.threads {
                        }
                    }
                }
            }
            page {
                id:3;
                title:"Output sequences";
                parameters-area {
                    group {
                        title:"Result files";
                        label-size:150;
                        write-sequence.url-out {
                            label:"Direct strand repeat units";
                        }
                        write-sequence-1.url-out {
                            label:"Compl. strand repeat units";
                        }
                    }
                }
            }
        }
    }
}