#@UGENE_WORKFLOW
#The workflow does the following things:
#1) Reads a set of Sanger sequencing reads from ABI files.
#2) Trims ends of the reads by the quality value.
#3) Filter the short trimmed reads.
#4) Aligns the filtered trimmed reads to a reference sequence.
#
#You can change the workflow parameters:
#1) Quality threshold for the trimming.
#2) Minimum read length. If length of a trimmed read is less than the minimum value than the read is filtered.
#
#The output data are:
#1) Multiple sequence alignment file. The first sequence of the alignment is the reference and other ones are the reads.
#2) Annotated reference sequence file. The annotations are the aligned reads.

include "Read one sequence.usa" as "Script-Read one sequence"

workflow "Trim and map Sanger reads"{

    SequenceQualityTrim {
        type:SequenceQualityTrim;
        name:"Sequence Quality Trimmer";
        both-ends:true;
    }
    read-sequence {
        type:read-sequence;
        name:"Read Sequence";
        url-in {
            dataset:"Dataset 1";
        }
    }
    align-to-reference {
        type:align-to-reference;
        name:"Map to Reference";
        result-url:alignment.ugenedb;
    }

    .actor-bindings {
        SequenceQualityTrim.out-sequence->align-to-reference.in-sequence
        read-sequence.out-sequence->SequenceQualityTrim.in-sequence
    }

    read-sequence.sequence->SequenceQualityTrim.in-sequence.sequence
    SequenceQualityTrim.sequence->align-to-reference.in-sequence.sequence

    .meta {
        parameter-aliases {
            SequenceQualityTrim.len-id {
                alias:min-length;
            }
            SequenceQualityTrim.qual-id {
                alias:threshold;
            }
            read-sequence.url-in {
                alias:reads;
            }
            align-to-reference.reference {
                alias:reference;
            }
            align-to-reference.result-url {
                alias:result-url;
            }
        }
        visual {
            SequenceQualityTrim {
                pos:"-720 -570";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-sequence.angle:180;
                out-sequence.angle:360;
            }
            align-to-reference {
                pos:"-420 -555";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-sequence.angle:180;
                out.angle:360;
            }
            read-sequence {
                pos:"-975 -555";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-sequence.angle:360;
            }
            SequenceQualityTrim.out-sequence->align-to-reference.in-sequence {
                text-pos:"-45 -43";
            }
            read-sequence.out-sequence->SequenceQualityTrim.in-sequence {
                text-pos:"-33.8281 -27";
            }
        }
        wizard {
            help-page-id:65930523;
	    auto-run: true;
            name:"Map Sanger Reads to Reference";
            page {
                id:1;
                next:2;
                title:"Reference Sequence";
                parameters-area {
                    group {
                        title:"Input file";
                        label-size:120;
                        align-to-reference.reference {
                            label:"Reference";
                        }
                    }
                }
            }
            page {
                id:2;
                next:3;
                title:"Input Sanger Reads (ABI Files)";
                parameters-area {
                    read-sequence.url-in {
                        type:datasets;
                    }
                }
            }
            page {
                id:3;
                next:4;
                title:"Mapping Settings";
                parameters-area {
                    group {
                        title:"Settings";
                        label-size:220;
                        SequenceQualityTrim.qual-id {
                        }
                        align-to-reference.identity {
                        }
                        align-to-reference.row-naming-policy {
                        }
                    }
                }
            }
            page {
                id:4;
                title:"Results";
                parameters-area {
                    group {
                        title:"Output files";
                        label-size:120;
                        align-to-reference.result-url {
                            label:"Mapped reads file";
                        }
                    }
                }
            }
        }
    }
}