#@UGENE_WORKFLOW
#This workflows allows one to extract a coverage and/or bases count from an assembly. It receives a number of assemblies and for each of them produces coverage as a tab delimited plain text file. The coverage is extracted considering a threshold value.



workflow "Extract Coverage"{

    read-assembly {
        type:read-assembly;
        name:"Read Assembly";
        url-in {
            dataset:"Dataset 1";
        }
    }
    extract-assembly-coverage {
        type:extract-assembly-coverage;
        name:"Extract Coverage from Assembly";
    }

    .actor-bindings {
        read-assembly.out-assembly->extract-assembly-coverage.in-assembly
    }

    read-assembly.assembly->extract-assembly-coverage.in-assembly.assembly

    .meta {
        parameter-aliases {
            read-assembly.url-in {
                alias:in-assembly;
                description:"An input assembly";
            }
            extract-assembly-coverage.export-type {
                alias:export-type;
                description:"The export type, possible values: 'coverage', 'bases count'. It is a single string, types are separated with comma. This parameter is used for 'Per base' format only.";
            }
            extract-assembly-coverage.format {
                alias:format;
                description:"The export format, possible values: '0 - Histogram', '1 - Per base', '2 - Bedgraph'";
            }
            extract-assembly-coverage.threshold {
                alias:threshold;
                description:"A threshold value";
            }
            extract-assembly-coverage.url-out {
                alias:url-out;
                description:"An URL to the output file";
            }
        }
        visual {
            extract-assembly-coverage {
                pos:"-420 -465";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-assembly.angle:180;
            }
            read-assembly {
                pos:"-705 -465";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-assembly.angle:360;
            }
            read-assembly.out-assembly->extract-assembly-coverage.in-assembly {
                text-pos:"-34.1406 -27";
            }
        }
        wizard {
            name:"Extract the assembly coverage and / or bases count";
            page {
                id:1;
                next:2;
                title:"Input assembly(-ies)";
                parameters-area {
                    read-assembly.url-in {
                        type:datasets;
                    }
                }
            }
            page {
                id:2;
                next:3;
                title:"Extract parameters";
                parameters-area {
                    group {
                        title:"Extract coverage parameters";
                        label-size:120;
                        extract-assembly-coverage.export-type {
                        }
                        extract-assembly-coverage.threshold {
                        }
                    }
                }
            }
            page {
                id:3;
                title:"Output data";
                parameters-area {
                    group {
                        title:"Output data";
                        label-size:120;
                        extract-assembly-coverage.url-out {
                            label:"Result file";
                        }
                    }
                }
            }
        }
    }
}