#@UGENE_WORKFLOW
#The workflow takes FASTQ files as input and process this data as follows:
#    - Filters the input sequencing reads by the CASAVA header (for Illumina platform).
#    - Cuts of adapter sequences.
#    - Trims the sequencing reads by quality.
#    - Merges different FASTQ files.
#    - [Optionally] Maps the sequencing reads by TopHat. You can skip this step, if after running this workflow you’re going to analyze the data with the Tuxedo workflow.
#
#The workflow also performs quality control of the data with FastQC: first, on the input FASTQ files and, second, after the pre-processing step.
#
#Besides intermediate files and FastQC reports, the final result of the workflow running is a merged FASTQ file. If mapping was selected, the output would also contain a BAM file with aligned reads and other TopHat output files.
#


workflow "Raw RNA-Seq data processing" {
    .meta {
        wizard {
            help-page-id:16122727;
            auto-run: true;
            has-run-button: false;
            has-defaults-button: false;
            name: "Configure Raw RNA-Seq Data Processing";
            finish-label: "Setup";
            result {
                NGS/raw_ngs/rnaseq/rnaseq_single.uwl: "tags.single topHatAlignment.with";
                NGS/raw_ngs/rnaseq/rnaseq_paired.uwl: "tags.paired topHatAlignment.with";
                NGS/raw_ngs/rnaseq/rnaseq_filtration_single.uwl: "tags.single topHatAlignment.without";
                NGS/raw_ngs/rnaseq/rnaseq_filtration_paired.uwl: "tags.paired topHatAlignment.without";
            }
            page {
                id: 1;
                title: "General settings";
                parameters-area {
                    group {
                        title:"Analysis type";
                        radio {
                            id: topHatAlignment;
                            value {
                                id: with;
                                label: "Include mapping with TopHat";
                            }
                            value {
                                id: without;
                                label: "Skip mapping";
                            }
                        }
                    }
                    group {
                        title: "Sequencing reads";
                        radio {
                            id: tags;
                            value {
                                id: single;
                                label: "Single-end";
                            }
                            value {
                                id: paired;
                                label: "Paired-end";
                            }
                        }
                    }
                }
            }
        }
    }
}