#@UGENE_WORKFLOW
#The workflow extracts unmapped reads from an input SAM/BAM file. Using the “samtools view –f 4” command the workflow returns unmapped reads in the BAM format by default.



workflow "Get unmapped reads"{

    filter-bam {
        type:filter-bam;
        name:"Filter BAM/SAM files";
        accept-flag:"The read is unmapped";
    }
    get-file-list {
        type:get-file-list;
        name:"SAM/BAM File List";
        url-in {
            dataset:"Dataset 1";
        }
    }

    .actor-bindings {
        get-file-list.out-url->filter-bam.in-file
    }

    get-file-list.url->filter-bam.in-file.url

    .meta {
        parameter-aliases {
            filter-bam.accept-flag {
                alias:f;
            }
            filter-bam.custom-dir {
                alias:out_dir;
            }
            filter-bam.flag {
                alias:F;
            }
            filter-bam.mapq {
                alias:q;
            }
            filter-bam.out-format {
                alias:format;
            }
            filter-bam.out-mode {
                alias:out_mode;
            }
            filter-bam.out-name {
                alias:out_name;
            }
            filter-bam.region {
                alias:r;
            }
            get-file-list.url-in {
                alias:in;
            }
        }
        visual {
            filter-bam {
                pos:"-546 -540";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-file.angle:180;
                out-file.angle:360;
            }
            get-file-list {
                pos:"-780 -540";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-url.angle:360;
            }
            get-file-list.out-url->filter-bam.in-file {
                text-pos:"-39.9844 -27";
            }
        }
        wizard {
            name:"Get Unmapped Reads";
            help-page-id:16123235;
            auto-run:true;
            page {
                id:1;
                next:2;
                title:"Input SAM/BAM File(s)";
                parameters-area {
                    get-file-list.url-in {
                        type:datasets;
                    }
                }
            }
            page {
                id:2;
                next:3;
                title:Filtration;
                parameters-area {
                    group {
                        title:Settings;
                        label-size:120;
                        filter-bam.accept-flag {
                        }
                        filter-bam.flag {
                        }
                        filter-bam.region {
                        }
                        filter-bam.mapq {
                        }
                    }
                }
            }
            page {
                id:3;
                title:Results;
                parameters-area {
                    group {
                        title:Output;
                        label-size:120;
                        filter-bam.out-mode {
                        }
                        filter-bam.custom-dir {
                        }
                        filter-bam.out-format {
                        }
                    }
                }
            }
        }
    }
}