#@UGENE_WORKFLOW
#This simple workflow finds patterns in you sequences and save them as annotations.
#
#You can use the workflow to map primers, regulatory signals, genes, etc.
#
#It loads any set of sequences from your files or folders and finds patterns in them. Just specify a dataset for the algorithm in the "Read sequence" element.
#
#Patterns are entered in comma-delimited format in the corresponding field of the "Find Pattern" element. Also you can load patterns from a file. In that case names of patterns can be saved as names of annotations. Files with patterns can be in any sequence format or in newline-delimited format.



workflow "Find patterns"{
    read-sequence {
        type:read-sequence;
        name:"Read Sequence";
        url-in {
            dataset:Dataset;
        }
    }
    search {
        type:search;
        name:"Find Pattern";
        result-name:misc_feature;
        use-names:true;
    }
    write-sequence {
        type:write-sequence;
        name:"Write Sequence";
        document-format:genbank;
        write-mode:0;
        url-out:annotations.gb;
    }


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

    read-sequence.sequence->search.in-sequence.sequence
    read-sequence.annotations->write-sequence.in-sequence.annotations
    search.annotations->write-sequence.in-sequence.annotations
    read-sequence.sequence->write-sequence.in-sequence.sequence

    .meta {
        visual {
            read-sequence {
                pos:"-855 -645";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-sequence.angle:360;
            }
            search {
                pos:"-660 -645";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-sequence.angle:180;
                out-annotations.angle:360;
            }
            write-sequence {
                pos:"-375 -645";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-sequence.angle:180;
            }
            read-sequence.out-sequence->search.in-sequence {
                text-pos:"-27.5 -24";
            }
            search.out-annotations->write-sequence.in-sequence {
                text-pos:"-45 -37";
            }
        }
        wizard {
            name:"Find patterns Wizard";
            help-page-id:16122701;
            auto-run: true;
            page {
                id:1;
                next:2;
                title:"Input sequence(s)";
                parameters-area {
                    read-sequence.url-in {
                        type:datasets;
                    }
                }
            }
            page {
                id:2;
                next:3;
                title:"Find Pattern";
                parameters-area {
                    group {
                        title:"Find Pattern parameters";
                        label-size:150;
                        search.pattern_file {
                            label:"Pattern";
                        }
                        search.result-name {
                        }
                        search.use-names {
                        }
                        search.max-mismatches-num {
                        }
                        search.allow-ins-del {
                        }
                        search.amino {
                        }
                        search.ambiguous {
                        }
                        search.pattern-name-qual {
                            label:"Qualifier name";
                        }
                    }
                }
            }
            page {
                id:3;
                title:"Output data";
                parameters-area {
                    group {
                        title:"Output data";
                        label-size:120;
                        write-sequence.url-out {
                            label:"Result file";
                        }
                        write-sequence.accumulate {
                            label:"Accumulate results";
                        }
                    }
                }
            }
        }
    }
}