#@UGENE_WORKFLOW
#Performs multiple sequence alignment with MUSCLE algorithm and saves the resulting alignment to document. Source data can be of any format containing sequences or alignments.
#
#To use this workflow, you need to specify locations for input and output file(s). To do this, select a corresponding task, so its' parameters appear in Property Inspector panel, and specify desired value(s) for "URL" parameter. Then you can launch the workflow with pressing Ctrl+R keys.

workflow "Align sequences with MUSCLE"{
    read-msa {
        type:read-msa;
        name:"Read alignment";
    }
    muscle {
        type:muscle;
        name:"Align with MUSCLE";
    }
    write-msa {
        type:write-msa;
        name:"Write alignment";
        document-format:clustal;
        url-out:muscle_alignment.aln;
    }


    .actor-bindings {
        read-msa.out-msa->muscle.in-msa
        muscle.out-msa->write-msa.in-msa
    }

    read-msa.msa->muscle.in-msa.msa
    muscle.msa->write-msa.in-msa.msa

    .meta {
        visual {
            read-msa {
                pos:"-645 -555";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-msa.angle:360;
            }
            muscle {
                pos:"-480 -555";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-msa.angle:180;
                out-msa.angle:360;
            }
            write-msa {
                pos:"-240 -555";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-msa.angle:180;
            }
            read-msa.out-msa->muscle.in-msa {
                text-pos:"-45 -50";
            }
            muscle.out-msa->write-msa.in-msa {
                text-pos:"-45 -50";
            }
        }
        wizard {
            name:"Align Sequences with MUSCLE Wizard";
            help-page-id:16122700;
            auto-run: true;
            page {
                id:1;
                next:2;
                title:"Input MSA(s)";
                parameters-area {
                    read-msa.url-in {
                        type:datasets;
                    }
                }
            }
            page {
                id:2;
                title:"Align Sequences with MUSCLE";
                parameters-area {
                    group {
                        title:"MUSCLE Algorithm parameters";
                        label-size:120;
                        muscle.mode {
                        }
                        muscle.stable {
                        }
                        muscle.max-iterations {
                        }
                        muscle.range {
                        }
                    }
                    group {
                        title:"Output File";
                        label-size:120;
                        write-msa.url-out {
                            label:"Result alignment";
                        }
                        write-msa.document-format {
                        }
                    }
                }
            }
        }
    }
}