#@UGENE_WORKFLOW
#To use this workflow input a set of sequences and set a minimum sequence length.
#All sequences with length less than the specified value will be filtered out. The result will be written into a FASTA file by default.

include "LengthMarker.usa" as "Script-LengthMarker"

workflow "Filter out short sequences"{

    read-sequence {
        type:read-sequence;
        name:"Read Sequence";
        url-in {
            dataset:"Dataset 1";
        }
    }
    filter-by-values {
        type:filter-by-values;
        name:Filter;
        text:long;
    }
    Script-LengthMarker {
        type:Script-LengthMarker;
        name:"Length Marker";
        script {
var seqObject = new Sequence(in_sequence);
if (seqObject.length() < SequenceLength) {
    out_text = 'short';
} else {
    out_text = 'long';
};
        };
        SequenceLength:10000;
    }
    write-sequence {
        type:write-sequence;
        name:"Write Long Sequences";
    }

    .actor-bindings {
        filter-by-values.filtered-data->write-sequence.in-sequence
        Script-LengthMarker.out->filter-by-values.in-data
        read-sequence.out-sequence->Script-LengthMarker.in
    }

    Script-LengthMarker.text->filter-by-values.in-data.text
    read-sequence.sequence->Script-LengthMarker.in.sequence
    read-sequence.sequence->write-sequence.in-sequence.sequence {
        path-through:filter-by-values;
    }

    .meta {
        visual {
            Script-LengthMarker {
                pos:"-615 -465";
                style:simple;
                bg-color-simple:"0 128 128 64";
                in.angle:180;
                out.angle:360;
            }
            filter-by-values {
                pos:"-450 -465";
                style:ext;
                bg-color-ext:"0 129 94 64";
                filtered-data.angle:360;
                in-data.angle:180;
            }
            read-sequence {
                pos:"-810 -465";
                style:ext;
                bg-color-ext:"255 170 127 64";
                out-sequence.angle:360;
            }
            write-sequence {
                pos:"-195 -465";
                style:ext;
                bg-color-ext:"170 170 0 64";
                in-sequence.angle:180;
            }
            Script-LengthMarker.out->filter-by-values.in-data {
                text-pos:"-40.5 -37";
            }
            filter-by-values.filtered-data->write-sequence.in-sequence {
                text-pos:"-39 -36";
            }
            read-sequence.out-sequence->Script-LengthMarker.in {
                text-pos:"-30.5 -39";
            }
        }
        wizard {
            name:"Filter short sequences";
            auto-run: true;
            page {
                id:1;
                next:2;
                title:"Input sequence(s)";
                parameters-area {
                    read-sequence.url-in {
                        type:datasets;
                    }
                }
            }
            page {
                id:2;
                next:3;
                title:Filtering;
                parameters-area {
                    group {
                        title:"Sequence Length Threshold";
                        label-size:150;
                        Script-LengthMarker.SequenceLength {
                            label:"Minimum length";
                        }
                    }
                }
            }
            page {
                id:3;
                title:"Output data";
                parameters-area {
                    group {
                        title:"Output data";
                        label-size:120;
                        write-sequence.url-out {
                            label:"Result file";
                        }
                    }
                }
            }
        }
    }
}