#@UGENE_WORKFLOW



workflow "HMM Annotation"{

    read-sequence {
        type:read-sequence;
        name:"Sequence Database";
        url-in {
            dataset:"Dataset 1";
        }
    }
    sequences-to-msa {
        type:sequences-to-msa;
        name:"Join Sequences into Alignment";
    }
    hmm2-build {
        type:hmm2-build;
        name:"HMM Build";
    }
    read-sequence-1 {
        type:read-sequence;
        name:"Target Sequence";
        url-in {
            dataset:"Dataset 1";
        }
    }
    hmm2-search {
        type:hmm2-search;
        name:"HMM Search";
    }
    write-sequence {
        type:write-sequence;
        name:"Write Sequence";
        document-format:genbank;
    }
    write-annotations {
        type:write-annotations;
        name:"Write Annotations";
        document-format:csv;
        write_names:true;
    }


    .actor-bindings {
        sequences-to-msa.out-msa->hmm2-build.in-msa
        read-sequence.out-sequence->sequences-to-msa.in-sequence
        hmm2-build.out-hmm2->hmm2-search.in-hmm2
        read-sequence-1.out-sequence->hmm2-search.in-sequence
        hmm2-search.out-annotations->write-sequence.in-sequence
        hmm2-search.out-annotations->write-annotations.in-annotations
    }

    read-sequence.sequence->sequences-to-msa.in-sequence.sequence
    sequences-to-msa.msa->hmm2-build.in-msa.msa
    hmm2-build.hmm2-profile->hmm2-search.in-hmm2.hmm2-profile
    read-sequence-1.sequence->hmm2-search.in-sequence.sequence
    hmm2-search.annotations->write-sequence.in-sequence.annotations
    read-sequence-1.annotations->write-sequence.in-sequence.annotations
    read-sequence-1.sequence->write-sequence.in-sequence.sequence
    hmm2-search.annotations->write-annotations.in-annotations.annotations
    read-sequence-1.annotations->write-annotations.in-annotations.annotations
    read-sequence-1.sequence->write-annotations.in-annotations.sequence

    .meta {
        visual {
            hmm2-build {
                pos:"-238 -614";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-msa.angle:180;
                out-hmm2.angle:360;
            }
            hmm2-search {
                pos:"-48 -512";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-hmm2.angle:150;
                in-sequence.angle:210;
                out-annotations.angle:360;
            }
            read-sequence {
                pos:"-681 -663";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-sequence.angle:360;
            }
            read-sequence-1 {
                pos:"-279 -432";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-sequence.angle:360;
            }
            sequences-to-msa {
                pos:"-488 -664";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-sequence.angle:180;
                out-msa.angle:360;
            }
            write-annotations {
                pos:"234 -330";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-annotations.angle:180;
            }
            write-sequence {
                pos:"246 -511";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-sequence.angle:180;
            }
            hmm2-build.out-hmm2->hmm2-search.in-hmm2 {
                text-pos:"-32 -24";
            }
            hmm2-search.out-annotations->write-annotations.in-annotations {
                text-pos:"-45 -37";
            }
            hmm2-search.out-annotations->write-sequence.in-sequence {
                text-pos:"-45 -37";
            }
            read-sequence-1.out-sequence->hmm2-search.in-sequence {
                text-pos:"-27.5 -24";
            }
            read-sequence.out-sequence->sequences-to-msa.in-sequence {
                text-pos:"-27.5 -24";
            }
            sequences-to-msa.out-msa->hmm2-build.in-msa {
                text-pos:"-43.5 -24";
            }
        }
    }
}