#@UGENE_WORKFLOW
#The workflow gets one or several sequences as input. For each sequence it sends a request to the NCBI BLAST remote database to search for homologous nucleotide sequences.
#The following options are set to the BLAST search by default:
#  1) Nucleotide BLAST database is used.
#  2) The search is optimized for high similar sequences (i.e. the "Megablast" option is selected) as on the NCBI BLAST web site.
#  3) The maximum number of hits is set to 10.
#As the result of the BLAST each input sequence is annotated with the "blast result" annotations.
#These annotations are used to fetch the corresponding homologous sequences from the NCBI database based on the identifiers specified in the "blast result" annotations.
#The output homologous sequences and the original sequences, annotated by BLAST, are grouped by folders. Name of the corresponding original sequence is used as the folder name.

workflow "Remote BLASTing"{

    read-sequence {
        type:read-sequence;
        name:"Read Sequence(s)";
        url-in {
            dataset:"Dataset 1";
        }
    }
    write-sequence {
        type:write-sequence;
        name:"Write Original Sequence(s) with BLAST Annotations";
        document-format:genbank;
        url-out {
var re = /[\\\/]/;
var tokens = url.toString().split(re);
var dir = "";
if (tokens.length > 0) {
    dir = tokens[tokens.length-1] + "/";
}
url_out = dir + "orig_with_blast.gb"
        };
    }
    blast-ncbi {
        type:blast-ncbi;
        name:"Remote BLAST";
        megablast:true;
    }
    fetch-sequence-by-id-from-annotation {
        type:fetch-sequence-by-id-from-annotation;
        name:"Fetch Sequences by ID from BLAST Annotations";
    }
    write-sequence-1 {
        type:write-sequence;
        name:"Write Homologous Sequences";
        document-format:genbank;
        url-out {
var re = /[\\\/]/;
var tokens = url.toString().split(re);
var dir = "";
if (tokens.length > 0) {
    dir = tokens[tokens.length-1] + "/";
}
url_out = dir + "homologous.gb"
        };
    }

    .actor-bindings {
        read-sequence.out-sequence->blast-ncbi.in-sequence
        blast-ncbi.out-annotations->write-sequence.in-sequence
        blast-ncbi.out-annotations->fetch-sequence-by-id-from-annotation.in-annotations
        fetch-sequence-by-id-from-annotation.out-sequence->write-sequence-1.in-sequence
    }

    blast-ncbi.annotations->write-sequence.in-sequence.annotations
    read-sequence.annotations->write-sequence.in-sequence.annotations
    read-sequence.sequence->write-sequence.in-sequence.sequence
    read-sequence.sequence->blast-ncbi.in-sequence.sequence
    blast-ncbi.annotations->fetch-sequence-by-id-from-annotation.in-annotations.annotations
    fetch-sequence-by-id-from-annotation.annotations->write-sequence-1.in-sequence.annotations
    fetch-sequence-by-id-from-annotation.sequence->write-sequence-1.in-sequence.sequence

    .meta {
        visual {
            blast-ncbi {
                pos:"-627 -675";
                style:ext;
                bg-color-ext:"0 170 127 64";
                in-sequence.angle:180;
                out-annotations.angle:291.038;
            }
            fetch-sequence-by-id-from-annotation {
                pos:"-658 -497";
                style:ext;
                bg-color-ext:"0 97 0 64";
                bounds:"-30 -30 147 84";
                in-annotations.angle:28.3008;
                out-sequence.angle:303.69;
            }
            read-sequence {
                pos:"-866 -676";
                style:ext;
                bg-color-ext:"0 141 212 64";
                bounds:"-30 -30 86.25 69";
                out-sequence.angle:360;
            }
            write-sequence {
                pos:"-401 -498";
                style:ext;
                bg-color-ext:"117 86 175 64";
                bounds:"-30 -30 121.25 79";
                in-sequence.angle:74.876;
            }
            write-sequence-1 {
                pos:"-654 -293";
                style:ext;
                bg-color-ext:"117 86 175 64";
                bounds:"-30 -30 129.25 83";
                in-sequence.angle:29.9315;
            }
            blast-ncbi.out-annotations->fetch-sequence-by-id-from-annotation.in-annotations {
                text-pos:"-55 -13";
            }
            blast-ncbi.out-annotations->write-sequence.in-sequence {
                text-pos:"-15 -11";
            }
            fetch-sequence-by-id-from-annotation.out-sequence->write-sequence-1.in-sequence {
                text-pos:"-43.5 -12";
            }
            read-sequence.out-sequence->blast-ncbi.in-sequence {
                text-pos:"-27.5 -24";
            }
        }
        wizard {
            name:"Remote BLASTing Wizard";
            help-page-id:16122736;
            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:"Remote Nucleotide BLAST";
                parameters-area {
                    group {
                        title:"Remote BLAST Parameters";
                        label-size:120;

                        blast-ncbi.db {}
                        blast-ncbi.e-value {}
                        blast-ncbi.hits {}
                        blast-ncbi.megablast {}
                    }
                    group {
                        title:"Additional";
                        label-size:120;
                        type:hideable;

                        blast-ncbi.gap_costs {}
                        blast-ncbi.match_scores {}
                        blast-ncbi.short_seq {}
                        blast-ncbi.entrez_query {}
                        blast-ncbi.result-name {}
                    }
                }
            }
            page {
                id:3;
                title:"Output Files";
                parameters-area {
                    label {
                        text:"For each input sequence the workflow outputs the sequence itself with the BLAST result annotations (named 'orig_with_blast.gb') and a set of homologous sequences loaded from the NCBI by IDs specified in the BLAST results (named 'homologous.gb').\n\nThe output files are grouped by folders, named as the input sequences, so that the results from different sequences can be clearly distinguished.";
                        background-color:"rgb(203,222,228)";
                    }
                }
            }
        }
    }
}