#@UGENE_WORKFLOW
# Runs a HMM search over sample sequence and saves results as annotations using Genbank file format. 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 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"{

    read-sequence {
        type:read-sequence;
        name:"Read Sequence";
        url-in {
            dataset:"Dataset 1";
        }
    }
    hmm3-search {
        type:hmm3-search;
        name:"HMM3 Search";
    }
    write-annotations {
        type:write-annotations;
        name:"Write Annotations";
        url-out:"";
        write-mode:0;
    }
    get-file-list {
        type:get-file-list;
        name:"Read File URL(s)";
        url-in {
            dataset:"Dataset 1";
        }
    }

    .actor-bindings {
        hmm3-search.out-annotations->write-annotations.in-annotations
        get-file-list.out-url->hmm3-search.in-hmm3
        read-sequence.out-sequence->hmm3-search.in-sequence
    }

    get-file-list.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 {
            read-sequence.url-in {
                alias:in-seq;
            }
            write-annotations.document-format {
                alias:format;
                description:"Annotations document format. Default: 'genbank'.";
            }
            write-annotations.url-out {
                alias:out;
                description:"Output file with annotations";
            }
            get-file-list.url-in {
                alias:in-hmm;
                description:"Input profile HMM";
            }
        }
        visual {
            get-file-list {
                pos:"-870 -555";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-url.angle:360;
            }
            hmm3-search {
                pos:"-570 -405";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-hmm3.angle:150;
                in-sequence.angle:210;
                out-annotations.angle:360;
            }
            read-sequence {
                pos:"-870 -390";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-sequence.angle:360;
            }
            write-annotations {
                pos:"-240 -405";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-annotations.angle:180;
            }
            get-file-list.out-url->hmm3-search.in-hmm3 {
                text-pos:"-45 -48";
            }
            hmm3-search.out-annotations->write-annotations.in-annotations {
                text-pos:"-45 -37";
            }
            read-sequence.out-sequence->hmm3-search.in-sequence {
                text-pos:"-27.5 -24";
            }
        }
    }
}