name        "LinkOut - find entries in a different NCBI database"
icon    "$BIRCH/public_html/images/birch_black_ico.png"
tip    "Find entries related to the existing query, in a different NCBI database"

var "in1"
    type        tempfile
    direction   in
    format      tsv
    save        true
            
tabset
    # - - - - - - - - - - - - - - - - - - - - - - - 
    # Only databases for which there is a corresponding BioLegato
    # application remain uncommented. As BioLegato becomes able
    # to handle data from other databases, they will be uncommented.
    tab "Database"

        var "db"
            type        list
            label       "Database to search"
            default     0
            choices
                #"pubmed"    "pubmed"
                "protein"    "protein"
                "nuccore"    "nuccore"
                "nucleotide"    "nucleotide"
                "nucgss"    "nucgss"
                "nucest"    "nucest"
                #"structure"    "structure"
                #"genome"    "genome"
                #"assembly"    "assembly"
                #"genomeprj"    "genomeprj"
                #"bioproject"    "bioproject"
                #"biosample"    "biosample"
                #"blastdbinfo"    "blastdbinfo"
                #"books"    "books"
                #"cdd"    "cdd"
                #"clinvar"    "clinvar"
                #"clone"    "clone"
                #"gap"    "gap"
                #"gapplus"    "gapplus"
                #"dbvar"    "dbvar"
                #"epigenomics"    "epigenomics"
                #"gene"    "gene"
                #"gds"    "gds"
                #"geoprofiles"    "geoprofiles"
                #"homologene"    "homologene"
                #"medgen"    "medgen"
                #"journals"    "journals"
                #"mesh"    "mesh"
                #"ncbisearch"    "ncbisearch"
                #"nlmcatalog"    "nlmcatalog"
                #"omim"    "omim"
                #"orgtrack"    "orgtrack"
                #"pmc"    "pmc"
                #"popset"    "popset"
                #"probe"    "probe"
                "proteinclusters"    "proteinclusters"
                #"pcassay"    "pcassay"
                #"biosystems"    "biosystems"
                #"pccompound"    "pccompound"
                #"pcsubstance"    "pcsubstance"
                #"pubmedhealth"    "pubmedhealth"
                #"seqannot"    "seqannot"
                #"snp"    "snp"
                #"sra"    "sra"
                #"taxonomy"    "taxonomy"
                #"toolkit"    "toolkit"
                #"toolkitall"    "toolkitall"
                #"toolkitbook"    "toolkitbook"
                "unigene"    "unigene"
                "unists"    "unists"
                #"gencoll"    "gencoll"
                #"gtr"    "gtr"



    # - - - - - - - - - - - - - - - - - - - - - - - 
    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 "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'"



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

panel
    var "Run"
        type        button
        label       "Run"
        shell       "ncbiquery --qfile %in1% --target %DB% --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