name        "RELATED - find related sequences in the NCBI nucleotide databases"
icon    "$BIRCH/public_html/images/birch_black_ico.png"
tip    "Find sequences related to the existing query, in the nucleotide database"

var "in1"
    type        tempfile
    direction   in
    format      tsv
    save        true


tabset
    # - - - - - - - - - - - - - - - - - - - - - - - 
    tab "Limits"

        var "SLEN"
            type    chooser
            label   "Limit sequence length?"
            default 0
            choices
                "Yes"    "AND %minlen%:%maxlen%[SLEN]"
                "No"    ""

        var "minlen"
            type        number
            label       "Min. Seq. Length"
            min         1
            max         1000000000
            default     1
        var "maxlen"
            type        number
            label       "Max. Seq. Length"
            min         1
            max         1000000000
            default     500000

        var "maxcount"
            type        number
            label       "Do not retrieve entries if number exceeds"
            min         1
            max         1000000000
            default     500

    # - - - - - - - - - - - - - - - - - - - - - - - 
    tab "Output"

        var "outfile"
            type        text
            label       "Output file name"

        var "outformat"
            type        combobox
            label       "OUTPUT FORMAT"
            default     0
            choices
                "Summary"     "docsum"
                "GI number"     "uid"
                "GenBank"     "gb"
                "GenBank with complete Contigs" "gbwithparts"
                "fasta"     "fasta"

        var "where"
            type        chooser
            label       "WHERE TO SEND OUTPUT"
            default     0
            choices
                "blncbi"     "(blncbi %in1%.tsv; sleep 5; rm %in1%*)"
                "Textedit window" "($BL_TextEditor %in1%.tsv; sleep 5; rm %in1%*) "
                "Output file" "mv %in1%.tsv %OUTFILE%; sleep 5; rm %in1%*;  echo ' NCBIQUERY completed'"



panel
    var "Run"
        type        button
        label       "Run"
        shell       "ncbiquery --qfile %in1% --related --format %OUTFORMAT% --maxcount %maxcount% --out %in1%.tsv; %WHERE%"
        close       true
    var "Help"
        type        button
        label       "Help"
        shell       "$BIRCH/script/chooseviewer.py http://www.ncbi.nlm.nih.gov/books/NBK25500/"
        close       false