#@UGENE_WORKFLOW
#The workflow uses the SnpEff tool to annotate and predict the effects of genetic variations (such as amino acid changes).
#
#To use the workflow you're required to input at least one file with variations (SNPs, insertions, deletions, and MNPs). The input file is usually obtained as a result of a sequencing experiment, and it is usually in Variant Call Format (VCF).
#
#To analyze the input variations SnpEff requires the variations file to have a certain chromosome notation. For example, "chr1" specified for a variation works fine, but "NC_000001" will result in an error. Therefore, the workflow contains an automated way for changing the chromosomes notation, which can be tweaked, if required.
#
#SnpEff outputs the annotated variations file and a detailed HTML report.



workflow "Variation annotation with SnpEff"{

    get-file-list {
        type:get-file-list;
        name:"Input Variations File";
        url-in {
            dataset:"Dataset 1";
        }
    }
    seff {
        type:seff;
        name:"Annotate and Predict Effects with SnpEff";
        out-mode:1;
    }
    rename-chromosome-in-variation {
        type:rename-chromosome-in-variation;
        name:"Change Chromosome Notation for Variations File";
        prefix-replace-with:chr;
        prefixes-to-replace:"NC_00000;NC_0000";
    }

    .actor-bindings {
        get-file-list.out-url->rename-chromosome-in-variation.in-file
        rename-chromosome-in-variation.out-file->seff.in-file
    }

    rename-chromosome-in-variation.url->seff.in-file.url
    get-file-list.url->rename-chromosome-in-variation.in-file.url

    .meta {
        parameter-aliases {
            get-file-list.url-in {
                alias:in;
            }
            seff.canon {
                alias:canon;
            }
            seff.custom-dir {
                alias:out_dir;
            }
            seff.genome {
                alias:genome;
            }
            seff.hgvs {
                alias:hgvs;
            }
            seff.lof {
                alias:lof;
            }
            seff.motif {
                alias:motif;
            }
            seff.out-mode {
                alias:mode;
            }
            seff.updown-length {
                alias:upDown;
            }
        }
        visual {
            get-file-list {
                pos:"-873 -501";
                style:ext;
                bg-color-ext:"42 108 251 64";
                bounds:"-30 -30 108.25 97";
                out-url.angle:349.38;
            }
            rename-chromosome-in-variation {
                pos:"-608 -513";
                style:ext;
                bg-color-ext:"128 104 117 64";
                bounds:"-30 -30 160 136";
                in-file.angle:228.094;
                out-file.angle:347.905;
            }
            seff {
                pos:"-268 -514";
                style:ext;
                bg-color-ext:"0 128 64 64";
                bounds:"-30 -30 141 130";
                in-file.angle:228.945;
                out-file.angle:345.256;
            }
            get-file-list.out-url->rename-chromosome-in-variation.in-file {
                text-pos:"-42.9844 -27";
            }
            rename-chromosome-in-variation.out-file->seff.in-file {
                text-pos:"-45 -43";
            }
        }
        wizard {
            name:"Variation Annotation with SnpEff Wizard";
            help-page-id:16122730;
            page {
                id:1;
                next:2;
                title:"Input variations";
                parameters-area {
                    group {
                        title:"Input file(s)";
                        get-file-list.url-in {
                            type:datasets;
                        }
                    }
                }
            }
            page {
                id:2;
                next:3;
                title:"Change chromosome notation for variations";
                parameters-area {
                    group {
                        title:Parameters;
                        label-size:150;
                        rename-chromosome-in-variation.prefixes-to-replace {
                        }
                        rename-chromosome-in-variation.prefix-replace-with {
                        }
                    }
                }
            }
            page {
                id:3;
                next:4;
                title:"SnpEff parameters";
                parameters-area {
                    group {
                        title:Parameters;
                        label-size:200;
                        seff.genome {
                        }
                    }
                    group {
                        title:Additional;
                        label-size:200;
                        type:hideable;
                        seff.canon {
                        }
                        seff.hgvs {
                        }
                        seff.lof {
                        }
                        seff.motif {
                        }
                        seff.updown-length {
                        }
                    }
                }
            }
            page {
                id:4;
                title:Output;
                parameters-area {
                    group {
                        title:"Output folder";
                        label-size:100;
                        seff.out-mode {
                        }
                        seff.custom-dir {
                        }
                    }
                }
            }
        }
    }
}