#@UGENE_WORKFLOW
#The workflow takes a nucleotide sequence as input and returns two files: translations of the sequence and translations of the complement sequence.



workflow "Get amino translations of a sequence"{

    sequence-translation {
        type:sequence-translation;
        name:"Amino Translation of Direct";
    }
    read-sequence {
        type:read-sequence;
        name:"Read Sequence";
        url-in {
            dataset:"Dataset 1";
        }
    }
    reverse-complement {
        type:reverse-complement;
        name:Complement;
    }
    sequence-translation-1 {
        type:sequence-translation;
        name:"Amino Translation of Complement";
    }
    write-sequence {
        type:write-sequence;
        name:"Write Direct Translations";
        url-out:direct_translations.fa;
    }
    write-sequence-1 {
        type:write-sequence;
        name:"Write Complement Translations";
        url-out:compl_translations.fa;
    }

    .actor-bindings {
        sequence-translation.out-sequence->write-sequence.in-sequence
        read-sequence.out-sequence->sequence-translation.in-sequence
        read-sequence.out-sequence->reverse-complement.in-sequence
        reverse-complement.out-sequence->sequence-translation-1.in-sequence
        sequence-translation-1.out-sequence->write-sequence-1.in-sequence
    }

    read-sequence.sequence->sequence-translation.in-sequence.sequence
    read-sequence.sequence->reverse-complement.in-sequence.sequence
    reverse-complement.sequence->sequence-translation-1.in-sequence.sequence
    sequence-translation.sequence->write-sequence.in-sequence.sequence
    sequence-translation-1.sequence->write-sequence-1.in-sequence.sequence

    .meta {
        visual {
            read-sequence {
                pos:"-649 -620";
                style:ext;
                bg-color-ext:"0 0 127 64";
                out-sequence.angle:360;
            }
            reverse-complement {
                pos:"-518 -448";
                style:ext;
                bg-color-ext:"85 170 255 64";
                in-sequence.angle:180;
                out-sequence.angle:358.176;
            }
            sequence-translation {
                pos:"-291 -619";
                style:ext;
                bg-color-ext:"0 129 94 64";
                in-sequence.angle:180;
                out-sequence.angle:360;
            }
            sequence-translation-1 {
                pos:"-281 -445";
                style:ext;
                bg-color-ext:"0 129 94 64";
                in-sequence.angle:180;
                out-sequence.angle:360;
            }
            write-sequence {
                pos:"-29 -620";
                style:ext;
                bg-color-ext:"85 85 0 64";
                bounds:"-30 -30 122.25 78";
                in-sequence.angle:180;
            }
            write-sequence-1 {
                pos:"-15 -447";
                style:ext;
                bg-color-ext:"85 85 0 64";
                bounds:"-30 -30 122.5 89";
                in-sequence.angle:180;
            }
            read-sequence.out-sequence->reverse-complement.in-sequence {
                text-pos:"9.5 -12";
            }
            read-sequence.out-sequence->sequence-translation.in-sequence {
                text-pos:"-29.5 -29";
            }
            reverse-complement.out-sequence->sequence-translation-1.in-sequence {
                text-pos:"-44 -43";
            }
            sequence-translation-1.out-sequence->write-sequence-1.in-sequence {
                text-pos:"-41 -31";
            }
            sequence-translation.out-sequence->write-sequence.in-sequence {
                text-pos:"-46 -28";
            }
        }
        wizard {
            name:"Get Amino Translations Wizard";
            help-page-id:16122701;
            auto-run: true;
            page {
                id:1;
                next:2;
                title:"Input sequence(s)";
                parameters-area {
                    read-sequence.url-in {
                        type:datasets;
                    }
                }
            }
            page {
                id:2;
                title:"Output data";
                parameters-area {
                    group {
                        title:"Result files";
                        label-size:120;
                        write-sequence.url-out {
                            label:"Direct translations";
                        }
                        write-sequence-1.url-out {
                            label:"Compl. translations";
                        }
                    }
                }
            }
        }
    }
}