#@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 align Sanger reads"{

    QualityTrim {
        type:QualityTrim;
        name:"FASTQ Quality Trimmer";
        both-ends:true;
        out-mode:1;
    }
    get-file-list {
        type:get-file-list;
        name:"File List";
        url-in {
            dataset:"Dataset 1";
        }
    }
    files-conversion {
        type:files-conversion;
        name:"To FASTQ";
        document-format:fastq;
        out-mode:1;
    }
    Script-Read-sequence {
        type:"Script-Read one sequence";
        name:"Read sequence";
        script {
out_sequence = null;
try {
    var sequences = readSequences(in_text);
    if (1 == sequences.length) {
        out_sequence = sequences[0];
    }
} catch (e) {
    print(e.toString());
}
        };
    }
    align-to-reference {
        type:align-to-reference;
        name:"Align to Reference";
    }
    write-msa {
        type:write-msa;
        name:"Write Alignment";
        url-out:"alignment.aln";
    }
    write-sequence {
        type:write-sequence;
        name:"Write Sequence";
        accumulate:false;
        document-format:genbank;
        url-out:"sequence.gb";
    }

    .actor-bindings {
        get-file-list.out-url->files-conversion.in-file
        QualityTrim.out-file->Script-Read-sequence.in
        files-conversion.out-file->QualityTrim.in-file
        Script-Read-sequence.out->align-to-reference.in-sequence
        align-to-reference.out->write-msa.in-msa
        align-to-reference.out->write-sequence.in-sequence
    }

    files-conversion.url->QualityTrim.in-file.url
    get-file-list.url->files-conversion.in-file.url
    QualityTrim.url->Script-Read-sequence.in.text
    Script-Read-sequence.sequence->align-to-reference.in-sequence.sequence
    align-to-reference.msa->write-msa.in-msa.msa
    align-to-reference.annotations->write-sequence.in-sequence.annotations
    align-to-reference.sequence->write-sequence.in-sequence.sequence

    .meta {
        parameter-aliases {
            QualityTrim.len-id {
                alias:min-length;
            }
            QualityTrim.qual-id {
                alias:threshold;
            }
            get-file-list.url-in {
                alias:reads;
            }
            align-to-reference.reference {
                alias:reference;
            }
            write-msa.url-out {
                alias:out-alignemnt;
            }
            write-msa.url-suffix {
                alias:alignment-suffix;
            }
            write-sequence.url-out {
                alias:out-seq;
            }
            write-sequence.url-suffix {
                alias:seq-suffix;
            }
        }
        visual {
            QualityTrim {
                pos:"-585 -510";
                style:ext;
                bg-color-ext:"208 69 0 64";
                in-file.angle:180;
                out-file.angle:296.206;
            }
            Script-Read-sequence {
                pos:"-540 -300";
                style:simple;
                bg-color-simple:"84 84 84 255";
                in.angle:93.6914;
                out.angle:360;
            }
            align-to-reference {
                pos:"-390 -300";
                style:ext;
                bg-color-ext:"0 128 0 64";
                in-sequence.angle:180;
                out.angle:360;
            }
            files-conversion {
                pos:"-750 -510";
                style:simple;
                bg-color-simple:"84 84 84 255";
                in-file.angle:177.917;
                out-file.angle:360;
            }
            get-file-list {
                pos:"-930 -510";
                style:ext;
                bg-color-ext:"24 102 175 64";
                out-url.angle:353.118;
            }
            write-msa {
                pos:"-120 -300";
                style:ext;
                bg-color-ext:"64 26 96 64";
                in-msa.angle:180;
            }
            write-sequence {
                pos:"-120 -510";
                style:ext;
                bg-color-ext:"64 26 96 64";
                in-sequence.angle:180;
            }
            QualityTrim.out-file->Script-Read-sequence.in {
                text-pos:"-31.5 -15";
            }
            Script-Read-sequence.out->align-to-reference.in-sequence {
                text-pos:"-30.5 -28";
            }
            align-to-reference.out->write-msa.in-msa {
                text-pos:"-34 -24";
            }
            align-to-reference.out->write-sequence.in-sequence {
                text-pos:"-31 -11";
            }
            files-conversion.out-file->QualityTrim.in-file {
                text-pos:"-12 -24";
            }
            get-file-list.out-url->files-conversion.in-file {
                text-pos:"-31 -24";
            }
        }
        wizard {
            help-page-id:16122701;    
	    auto-run: true;
            name:"Trim and Align Sanger Reads";
            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 {
                    get-file-list.url-in {
                        type:datasets;
                    }
                }
            }
            page {
                id:3;
                next:4;
                title:"Trimming and Filtering";
                parameters-area {
                    group {
                        title:"Settings";
                        label-size:120;
                        QualityTrim.qual-id {
                        }
                        QualityTrim.len-id {
                        }
                    }
                }
            }
            page {
                id:4;
                title:"Results";
                parameters-area {
                    group {
                        title:"Output files";
                        label-size:120;
                        write-msa.url-out {
                            label:"Aligned reads file";
                        }
                        write-sequence.url-out {
                            label:"Annotated sequence file";
                        }
                    }
                }
            }
        }
    }
}