#@UGENE_WORKFLOW
#Builds a new profile HMM from input alignment, calibrates the HMM and saves to a file. Then runs a test HMM search over sample sequence and saves test results to Genbank file. To run this workflow, you need to specify appropriate locations for input/output files. This is achieved by selecting a task and editing interesting parameters in Property Inspector panel.Optionally, fine tune the build/search parameters as you see fit. Then schedule the workflow for execution by pressing CTRL+R shortcut. You can watch its" progress in a Task View of UGENE.



workflow "New workflow"{

    hmm3-build {
        type:hmm3-build;
        name:"HMM3 Build";
    }
    hmm3-search {
        type:hmm3-search;
        name:"HMM3 Search";
    }
    write-annotations {
        type:write-annotations;
        name:"Write Annotations";
        url-out:"";
        write-mode:0;
    }
    read-sequence {
        type:read-sequence;
        name:"Read Sequence";
        url-in {
            dataset:"Dataset 1";
        }
    }
    read-msa {
        type:read-msa;
        name:"Read Alignment";
        url-in {
            dataset:"Dataset 1";
        }
    }

    .actor-bindings {
        read-msa.out-msa->hmm3-build.in-msa
        hmm3-build.out-hmm3->hmm3-search.in-hmm3
        hmm3-search.out-annotations->write-annotations.in-annotations
        read-sequence.out-sequence->hmm3-search.in-sequence
    }

    read-msa.msa->hmm3-build.in-msa.msa
    hmm3-build.url->hmm3-search.in-hmm3.url
    read-sequence.sequence->hmm3-search.in-sequence.sequence
    hmm3-search.annotations->write-annotations.in-annotations.annotations

    .meta {
        parameter-aliases {
            hmm3-search.e-val {
                alias:domE;
            }
            hmm3-search.filter-by {
                alias:filter_by;
            }
            hmm3-search.result-name {
                alias:annotation-name;
            }
            hmm3-search.score {
                alias:domT;
            }
            hmm3-search.seed {
                alias:seed;
            }
            write-annotations.document-format {
                alias:format;
            }
            write-annotations.url-out {
                alias:out;
            }
            read-sequence.url-in {
                alias:in_sequence;
            }
            read-msa.url-in {
                alias:in_alignment;
            }
        }
        visual {
            hmm3-build {
                pos:"-780 -570";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-msa.angle:180;
                out-hmm3.angle:360;
            }
            hmm3-search {
                pos:"-600 -435";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-hmm3.angle:150;
                in-sequence.angle:210;
                out-annotations.angle:360;
            }
            read-msa {
                pos:"-975 -570";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-msa.angle:360;
            }
            read-sequence {
                pos:"-780 -420";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-sequence.angle:360;
            }
            write-annotations {
                pos:"-360 -435";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-annotations.angle:180;
            }
            hmm3-build.out-hmm3->hmm3-search.in-hmm3 {
                text-pos:"-35 -24";
            }
            hmm3-search.out-annotations->write-annotations.in-annotations {
                text-pos:"-45 -37";
            }
            read-msa.out-msa->hmm3-build.in-msa {
                text-pos:"-45 -50";
            }
            read-sequence.out-sequence->hmm3-search.in-sequence {
                text-pos:"-27.5 -24";
            }
        }
    }
}