#@UGENE_WORKFLOW
#This workflow simulates the PCR process. You are required to input:
#1) File(s) with DNA sequences.
#2) A file with DNA sequences of primers pairs. The pairs must be ordered as follows:
#    a. The first sequence of the first pair.
#    b. The second sequence of the first pair.
#    c. The first sequence of the second pair.
#    d. The second sequence of the second pair.
#    e. etc.
#
#As the output data you will get:
#1) A file with the HTML report about the in silico PCR:
#    a. Products count table.
#    b. Pairs details.
#2) Files with the amplified PCR products.


workflow "In silico PCR"{

    in-silico-pcr {
        type:in-silico-pcr;
        name:"In Silico PCR";
        primers-url:"";
    }
    read-sequence {
        type:read-sequence;
        name:"Read Sequence";
        url-in {
            dataset:"Dataset 1";
        }
    }
    write-sequence {
        type:write-sequence;
        name:"Write Sequence";
        accumulate:false;
        document-format:genbank;
    }

    .actor-bindings {
        read-sequence.out-sequence->in-silico-pcr.in-sequence
        in-silico-pcr.out->write-sequence.in-sequence
    }

    read-sequence.annotations->in-silico-pcr.in-sequence.annotations
    read-sequence.sequence->in-silico-pcr.in-sequence.sequence
    in-silico-pcr.annotations->write-sequence.in-sequence.annotations
    in-silico-pcr.sequence->write-sequence.in-sequence.sequence

    .meta {
        parameter-aliases {
            in-silico-pcr.primers-url {
                alias:primers;
            }
            in-silico-pcr.report-url {
                alias:report;
            }
            read-sequence.url-in {
                alias:in;
            }
            write-sequence.url-out {
                alias:out;
            }
        }
        visual {
            in-silico-pcr {
                pos:"-465 -390";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-sequence.angle:180;
                out.angle:360;
            }
            read-sequence {
                pos:"-705 -390";
                style:ext;
                bg-color-ext:"24 102 175 64";
                out-sequence.angle:360;
            }
            write-sequence {
                pos:"-180 -390";
                style:ext;
                bg-color-ext:"64 26 96 64";
                in-sequence.angle:180;
            }
            in-silico-pcr.out->write-sequence.in-sequence {
                text-pos:"-34 -24";
            }
            read-sequence.out-sequence->in-silico-pcr.in-sequence {
                text-pos:"-27.5 -24";
            }
        }
        wizard {
            name:"In Silico PCR";
            help-page-id:16123482;
            auto-run: true;
            page {
                id:1;
                next:2;
                title:"Input DNA sequences";
                parameters-area {
                    read-sequence.url-in {
                        type:datasets;
                    }
                }
            }
            page {
                id:2;
                next:3;
                title:"Primers and parameters";
                parameters-area {
                    group {
                        title:Primers;
                        label-size:120;
                        in-silico-pcr.primers-url {
                        }
                    }
                    group {
                        title:"In silico PCR";
                        label-size:120;
                        in-silico-pcr.mismatches {
                        }
                        in-silico-pcr.perfect-match {
                        }
                        in-silico-pcr.max-product {
                        }
                    }
                }
            }
            page {
                id:3;
                title:"Output data";
                parameters-area {
                    label {
                        text:"The workflow output consists of the HTML report and the found amplified PCR products. File names of the products are based on the DNA sequence name and the primer names.";
                        background-color:"rgb(203,222,228)";
                    }
                }
            }
        }
    }
}