#@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 "Build HMM from alignment and test it"{
    read-sequence {
        type:read-sequence;
        name:"Read sequence";
        merge-gap:10;
        mode:0;
    }
    read-msa {
        type:read-msa;
        name:"Read alignment";
    }
    hmm2-build {
        type:hmm2-build;
        name:"HMM build";
        calibrate:true;
        calibration-threads:1;
        deviation:200;
        fix-samples-length:0;
        mean-samples-length:325;
        samples-num:5000;
        seed:0;
        strategy:1;
    }
    hmm2-write-profile {
        type:hmm2-write-profile;
        name:"Write HMM profile";
        write-mode:2;
        url-out:profile.hmm;
    }
    hmm2-search {
        type:hmm2-search;
        name:"HMM search";
        e-val:-1;
        result-name:hmm_signal;
        score:-1000000000;
        seqs-num:1;
    }
    write-genbank {
        type:write-sequence;
		document-format:genbank;
        name:"Write Genbank";
        accumulate:true;
        write-mode:2;
        url-out:output.gb;
    }

    read-msa.msa->hmm2-build.in-msa.msa
    hmm2-build.hmm2-profile->hmm2-write-profile.in-hmm2.hmm2-profile
    hmm2-build.hmm2-profile->hmm2-search.in-hmm2.hmm2-profile
    read-sequence.sequence->hmm2-search.in-sequence.sequence
    hmm2-search.annotations->write-genbank.in-sequence.annotations
    read-sequence.annotations->write-genbank.in-sequence.annotations
    read-sequence.sequence->write-genbank.in-sequence.sequence

    .meta {
        visual {
            read-sequence {
                pos:"-780 -525";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-sequence.angle:360;
            }
            read-msa {
                pos:"-780 -675";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-msa.angle:360;
            }
            hmm2-build {
                pos:"-630 -675";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-msa.angle:180;
                out-hmm2.angle:360;
            }
            hmm2-write-profile {
                pos:"-435 -675";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-hmm2.angle:180;
            }
            hmm2-search {
                pos:"-435 -540";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-hmm2.angle:150;
                in-sequence.angle:210;
                out-annotations.angle:360;
            }
            write-genbank {
                pos:"-195 -540";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-sequence.angle:180;
            }
            read-msa.out-msa->hmm2-build.in-msa {
                text-pos:"-45 -50";
            }
            hmm2-build.out-hmm2->hmm2-write-profile.in-hmm2 {
                text-pos:"-32 -24";
            }
            read-sequence.out-sequence->hmm2-search.in-sequence {
                text-pos:"-27.5 -24";
            }
            hmm2-build.out-hmm2->hmm2-search.in-hmm2 {
                text-pos:"-32 -24";
            }
            hmm2-search.out-annotations->write-genbank.in-sequence {
                text-pos:"-45 -37";
            }
        }
        wizard {
            name:"Build HMM from alignment and test it Wizard";
            help-page-id:16122715;
            page {
                id:1;
                next:2;
                title:"Input MSA(s)"
                parameters-area {
                    read-msa.url-in {
                        type:datasets;
                    }
                }
            }
            page {
                id:2;
                next:3;
                title:"Input sequence(s)";
                parameters-area {
                    read-sequence.url-in {
                        type:datasets;
                    }
                }
            }
            page {
                id:3;
                next:4;
                title:"HMM Build";
                parameters-area {
                    group {
                        title:"Output data";
                        label-size:120;
                        hmm2-write-profile.url-out {
                            label:"Output HMM profile";
                        }
                    }
                    group {
                        title:"HMM Build parameters";
                        label-size:120;
                        hmm2-build.strategy {
                        }
                        hmm2-build.profile-name {
                        }
                        hmm2-build.calibrate {
                        }
                    }
                    group {
                        title:"Additional";
                        label-size:120;
                        type:hideable;
                        hmm2-build.calibration-threads {
                        }
                        hmm2-build.fix-samples-length {
                            label:"Fixed length";
                        }
                        hmm2-build.mean-samples-length {
                            label:"Mean length";
                        }
                        hmm2-build.samples-num {
                        }
                        hmm2-build.deviation {
                        }
                        hmm2-build.seed {
                        }
                    }
                }
            }
            page {
                id:4;
                title:"HMM Search";
                parameters-area {
                    group {
                        title:"Output data";
                        label-size:120;
                        write-genbank.url-out {
                            label:"Output genbank";
                        }
                        write-genbank.accumulate {
                            label:"Accumulate results";
                        }
                    }
                    group {
                        title:"HMM Search parameters";
                        label-size:120;
                        hmm2-search.result-name {
                        }
                        hmm2-search.seqs-num {
                        }
                        hmm2-search.e-val {
                        }
                        hmm2-search.score {
                        }
                    }
                }
            }
        }
    }
}