# DO NOT EDIT THIS FILE!
# This file is automatically generated by blastdbkit.py during installation,
# update or by birchadmin --> UpdateAddInstall
name        "SEQFETCHlocal - Retrieve nucleotide FASTA entries from local database"
icon    "$BIRCH/public_html/images/birch_black_ico.png"
tip    "Retrieve nucleotide FASTA entries from local database"

var "dbase"
    type       combobox
    label      "Database"
    default    0
    choices
        "Non-redundant nucleotide (nt)" "-db nt"
        "RefSeq RNA" "-db refseq_rna"
        "Human Genomic - RefSeq Human chromosomal" "-db human_genome"
        "Mouse Genomic - RefSeq Mouse chromosomal" "-db mouse_genome"
        "Representative Eukaryotic Genomes" "-db ref_euk_rep_genomes"
        "Representative Prokaryotic Genomes" "-db ref_prok_rep_genomes"
        "Representative Viroid Genomes" "-db ref_viroids_rep_genomes"
        "Representative Virus Genomes" "-db ref_viruses_rep_genomes"
        "Patented Nucleotide (patnt)" "-db patnt"
        "Nucleotide sequences from PDB 3D nucl. acid structures (pdbnt)" "-db pdbnt"
        "16S ribosomal" "-db 16S_ribosomal_RNA"
        "18S_fungal_sequences" "-db 18S_fungal_sequences"
        "28S_fungal_sequences" "-db 28S_fungal_sequences"
        "ITS_RefSeq_Fungi" "-db ITS_RefSeq_Fungi"
        "ITS_eukaryote_sequences" "-db ITS_eukaryote_sequences"
        "LSU_eukaryote_rRNA" "-db LSU_eukaryote_rRNA"
        "LSU_prokaryote_rRNA" "-db LSU_prokaryote_rRNA"
        "SSU_eukaryote_rRNA" "-db SSU_eukaryote_rRNA"
        "Betacoronavirus" "-db Betacoronavirus"
        "Metagenomic - Nucleotide (env_nt)" "-db env_nt"
        "User-created file (FASTA format)" "-subject %USERFILE%"

var "userfile"
    type        file
    label       "filename"

var "where"
    type        chooser
    label       "WHERE TO SEND OUTPUT"
    default     0
    choices
        "bldna"     "(bldna %in1%.tmp; rm %in1%.*)"
        "Textedit window" "($BL_TextEditor %in1%.tmp; rm %in1%.*) "
        "Output file" "mv %in1%.tmp %OUTFILE%; rm %in1%.*;  echo ' SeqFetch completed'"
       
var "in1"
    type        tempfile
    direction   in
    format      tsv
    save        true
var "outfile"
    type        text
    label       "Output file name"
panel
    var "Run"
        type        button
        label       "Run"
        shell       "(grep -v '#' %in1% | tr -d '\042' |cut -f1 > %in1%.nam; (blastdbcmd %DBASE% -entry_batch %in1%.nam -out %in1%.tmp; %WHERE%))"
        close       true
    var "Help"
        type        button
        label       "Help"
        shell       "$BIRCH/script/chooseviewer.py http://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Entrez_Searching_Options"
        close       false