name "tbl2asn - Re-format annotated genome for submission to NCBI" icon "$BIRCH/pkg/NCBI/NCBI_tiny.png" tip "Convert .tbl files to .sqn (Sequin) files for submission to NCBI" var "in1" type tempfile direction in format tsv save false tabset # - - - - - - - Files and Directories - - - - - - - tab "Files" var "template" type file label "template file (.sbt) - REQUIRED" default "" var "suffix" type text label "Suffix for identifying FASTA files" default ".fsa" var "comment" type chooser label "Comments" default 0 choices "none" "" "Type comments below" "-y '%COMTEXT%'" "Read comments from a file" "-Y %COMFILE%" var "comtext" type text label " comments" default "" var "comfile" type file label " comment file" default "" var "vv" type chooser label "Write validation file (.val)?" default 0 choices "Yes" "v" "No" "" var "vb" type chooser label "Write GenBank file (.gbf)?" default 0 choices "Yes" "b" "No" "" var "vg" type chooser label "Generate gene report (.t2g)?" default 1 choices "Yes" "g" "No" "" var "resultdir" type dir label " Directory for results" default "../tbl2asn" var "sfout" type chooser label "Write all output to a single Sequin file?" default 1 choices "Yes" "-o %RESULTDIR%/%SFNAME%" "No" "" var "sfname" type text label " name for single output file (.sqn)" default "" # - - - - - - - Parameters - - - - - - - tab "Parameters" var "xa" type chooser label "Generate Definition lines automatically?" default 1 choices "Yes" "A" "No" "" var "xe" type chooser label "Treat like eukaryota in the Discrepancy Report?" default 1 choices "Yes" "E" "No" "" var "mastergenome" type combobox label "Master genome flags: " default 1 choices "none" "" "Normal (-M n)" "-M n" "Big sequence (-M b)" "-M b" "Power option (-M p)" "-M p" "TSA (-M t)" "-M t" var "rtax" type chooser label "Remote Taxonomy Lookup" default 1 choices "Yes" "-T" "No" "" var "localids" type chooser label "Force local protein_id/transcript_id?" default 0 choices "Yes" "-L" "No" "" var "gapanno" type combobox label "Gap annotation: " default 0 choices "Runs of 20+ Ns are gaps, 100 Ns are unknown length" "r20u" "Runs of 20+ Ns are gaps, 100 Ns are known length" "r20k" "Runs of 10+ Ns are gaps, 100 Ns are unknown length" "r10u" "Runs of 10+ Ns are gaps, 100 Ns are known length" "r10k" "FASTA Delta, di FASTA Delta with Implicit Gaps" "d" "FASTA with Gap Lines" "z" "PHRAP/ACE" "e" "ASN.1 for -M flag" "b" var "vr" type chooser label "Validate without country check?" default 1 choices "Yes" "r" "No" "" var "cf" type chooser label "Fix product names?" default 0 choices "Yes" "f" "No" "" var "cx" type chooser label "extend feature ends 1 or 2 nucl. past gaps or seq. ends?" default 1 choices "Yes" "x" "No" "" var "cd" type chooser label "Re-format date:" default 0 choices "Off" "" "Day first" "D" "Day first" "d" var "additional" type text label "additional tbl2asn options" default " " # - - - - - - - Source Qualifiers - - - - - - - # The fifth qualifier term, %Q5%, does not get parsed, # but all others do. I have done extensive testing of many # variants of this menu, and can't get it to work. This may # be due to an error in how BioLegato parses menus. See Q5 # below. tab "Qualifiers" var "sourcequal" type chooser label "Source qualifiers" default 0 choices "+" "%Q1% %Q2% %Q3% %Q4% %Q6% %Q7%" "-" "" panel var "q1" type chooser default 1 choices "+" " [%Q1FIELD%=%Q1VAL%]" "-" "" var "q1field" type combobox default 41 choices "acronym" "acronym" "altitude" "altitude" "anamorph" "anamorph" "authority" "authority" "bio-material" "bio-material" "biotype" "biotype" "biovar" "biovar" "breed" "breed" "cell-line" "cell-line" "cell-type" "cell-type" "chemovar" "chemovar" "chromosome" "chromosome" "clone" "clone" "clone-lib" "clone-lib" "collected-by" "collected-by" "collection-date" "collection-date" "common" "common" "country" "country" "cultivar" "cultivar" "culture-collection" "culture-collection" "dev-stage" "dev-stage" "ecotype" "ecotype" "endogenous-virus-name" "endogenous-virus-name" "forma" "forma" "forma-specialis" "forma-specialis" "fwd-PCR-primer-name" "fwd-PCR-primer-name" "fwd-PCR-primer-seq" "fwd-PCR-primer-seq" "genotype" "genotype" "group" "group" "haplogroup" "haplogroup" "haplotype" "haplotype" "host" "host" "identified-by" "identified-by" "isolate" "isolate" "isolation-source" "isolation-source" "lab-host" "lab-host" "lat-lon" "lat-lon" "linkage-group" "linkage-group" "map" "map" "mating-type" "mating-type" "note" "note" "organism" "organism" "pathovar" "pathovar" "plasmid-name" "plasmid-name" "plastid-name" "plastid-name" "pop-variant" "pop-variant" "rev-PCR-primer-name" "rev-PCR-primer-name" "rev-PCR-primer-seq" "rev-PCR-primer-seq" "segment" "segment" "serogroup" "serogroup" "serotype" "serotype" "serovar" "serovar" "sex" "sex" "specimen-voucher" "specimen-voucher" "strain" "strain" "sub-species" "sub-species" "subclone" "subclone" "subgroup" "subgroup" "substrain" "substrain" "subtype" "subtype" "synonym" "synonym" "teleomorph" "teleomorph" "tissue-lib" "tissue-lib" "tissue-type" "tissue-type" "type" "type" "variety" "variety" var "q1val" type text default "" panel var "q2" type chooser default 1 choices "+" " [%Q2FIELD%=%Q2VAL%]" "-" "" var "q2field" type combobox default 54 choices "acronym" "acronym" "altitude" "altitude" "anamorph" "anamorph" "authority" "authority" "bio-material" "bio-material" "biotype" "biotype" "biovar" "biovar" "breed" "breed" "cell-line" "cell-line" "cell-type" "cell-type" "chemovar" "chemovar" "chromosome" "chromosome" "clone" "clone" "clone-lib" "clone-lib" "collected-by" "collected-by" "collection-date" "collection-date" "common" "common" "country" "country" "cultivar" "cultivar" "culture-collection" "culture-collection" "dev-stage" "dev-stage" "ecotype" "ecotype" "endogenous-virus-name" "endogenous-virus-name" "forma" "forma" "forma-specialis" "forma-specialis" "fwd-PCR-primer-name" "fwd-PCR-primer-name" "fwd-PCR-primer-seq" "fwd-PCR-primer-seq" "genotype" "genotype" "group" "group" "haplogroup" "haplogroup" "haplotype" "haplotype" "host" "host" "identified-by" "identified-by" "isolate" "isolate" "isolation-source" "isolation-source" "lab-host" "lab-host" "lat-lon" "lat-lon" "linkage-group" "linkage-group" "map" "map" "mating-type" "mating-type" "note" "note" "organism" "organism" "pathovar" "pathovar" "plasmid-name" "plasmid-name" "plastid-name" "plastid-name" "pop-variant" "pop-variant" "rev-PCR-primer-name" "rev-PCR-primer-name" "rev-PCR-primer-seq" "rev-PCR-primer-seq" "segment" "segment" "serogroup" "serogroup" "serotype" "serotype" "serovar" "serovar" "sex" "sex" "specimen-voucher" "specimen-voucher" "strain" "strain" "sub-species" "sub-species" "subclone" "subclone" "subgroup" "subgroup" "substrain" "substrain" "subtype" "subtype" "synonym" "synonym" "teleomorph" "teleomorph" "tissue-lib" "tissue-lib" "tissue-type" "tissue-type" "type" "type" "variety" "variety" var "q2val" type text default "" panel var "q3" type chooser default 1 choices "+" " [%Q3FIELD%=%Q3VAL%]" "-" "" var "q3field" type combobox default 42 choices "acronym" "acronym" "altitude" "altitude" "anamorph" "anamorph" "authority" "authority" "bio-material" "bio-material" "biotype" "biotype" "biovar" "biovar" "breed" "breed" "cell-line" "cell-line" "cell-type" "cell-type" "chemovar" "chemovar" "chromosome" "chromosome" "clone" "clone" "clone-lib" "clone-lib" "collected-by" "collected-by" "collection-date" "collection-date" "common" "common" "country" "country" "cultivar" "cultivar" "culture-collection" "culture-collection" "dev-stage" "dev-stage" "ecotype" "ecotype" "endogenous-virus-name" "endogenous-virus-name" "forma" "forma" "forma-specialis" "forma-specialis" "fwd-PCR-primer-name" "fwd-PCR-primer-name" "fwd-PCR-primer-seq" "fwd-PCR-primer-seq" "genotype" "genotype" "group" "group" "haplogroup" "haplogroup" "haplotype" "haplotype" "host" "host" "identified-by" "identified-by" "isolate" "isolate" "isolation-source" "isolation-source" "lab-host" "lab-host" "lat-lon" "lat-lon" "linkage-group" "linkage-group" "map" "map" "mating-type" "mating-type" "note" "note" "organism" "organism" "pathovar" "pathovar" "plasmid-name" "plasmid-name" "plastid-name" "plastid-name" "pop-variant" "pop-variant" "rev-PCR-primer-name" "rev-PCR-primer-name" "rev-PCR-primer-seq" "rev-PCR-primer-seq" "segment" "segment" "serogroup" "serogroup" "serotype" "serotype" "serovar" "serovar" "sex" "sex" "specimen-voucher" "specimen-voucher" "strain" "strain" "sub-species" "sub-species" "subclone" "subclone" "subgroup" "subgroup" "substrain" "substrain" "subtype" "subtype" "synonym" "synonym" "teleomorph" "teleomorph" "tissue-lib" "tissue-lib" "tissue-type" "tissue-type" "type" "type" "variety" "variety" var "q3val" type text default "" panel var "q4" type chooser default 1 choices "+" " [%q4field%=%q4val%]" "-" "" var "q4field" type combobox default 42 choices "acronym" "acronym" "altitude" "altitude" "anamorph" "anamorph" "authority" "authority" "bio-material" "bio-material" "biotype" "biotype" "biovar" "biovar" "breed" "breed" "cell-line" "cell-line" "cell-type" "cell-type" "chemovar" "chemovar" "chromosome" "chromosome" "clone" "clone" "clone-lib" "clone-lib" "collected-by" "collected-by" "collection-date" "collection-date" "common" "common" "country" "country" "cultivar" "cultivar" "culture-collection" "culture-collection" "dev-stage" "dev-stage" "ecotype" "ecotype" "endogenous-virus-name" "endogenous-virus-name" "forma" "forma" "forma-specialis" "forma-specialis" "fwd-PCR-primer-name" "fwd-PCR-primer-name" "fwd-PCR-primer-seq" "fwd-PCR-primer-seq" "genotype" "genotype" "group" "group" "haplogroup" "haplogroup" "haplotype" "haplotype" "host" "host" "identified-by" "identified-by" "isolate" "isolate" "isolation-source" "isolation-source" "lab-host" "lab-host" "lat-lon" "lat-lon" "linkage-group" "linkage-group" "map" "map" "mating-type" "mating-type" "note" "note" "organism" "organism" "pathovar" "pathovar" "plasmid-name" "plasmid-name" "plastid-name" "plastid-name" "pop-variant" "pop-variant" "rev-PCR-primer-name" "rev-PCR-primer-name" "rev-PCR-primer-seq" "rev-PCR-primer-seq" "segment" "segment" "serogroup" "serogroup" "serotype" "serotype" "serovar" "serovar" "sex" "sex" "specimen-voucher" "specimen-voucher" "strain" "strain" "sub-species" "sub-species" "subclone" "subclone" "subgroup" "subgroup" "substrain" "substrain" "subtype" "subtype" "synonym" "synonym" "teleomorph" "teleomorph" "tissue-lib" "tissue-lib" "tissue-type" "tissue-type" "type" "type" "variety" "variety" var "q4val" type text default "" panel var "q5" type chooser default 1 choices "+" " [%Q5FIELD%=%Q5VAL%]" "-" "" var "q5field" type combobox default 42 choices "acronym" "acronym" "altitude" "altitude" "anamorph" "anamorph" "authority" "authority" "bio-material" "bio-material" "biotype" "biotype" "biovar" "biovar" "breed" "breed" "cell-line" "cell-line" "cell-type" "cell-type" "chemovar" "chemovar" "chromosome" "chromosome" "clone" "clone" "clone-lib" "clone-lib" "collected-by" "collected-by" "collection-date" "collection-date" "common" "common" "country" "country" "cultivar" "cultivar" "culture-collection" "culture-collection" "dev-stage" "dev-stage" "ecotype" "ecotype" "endogenous-virus-name" "endogenous-virus-name" "forma" "forma" "forma-specialis" "forma-specialis" "fwd-PCR-primer-name" "fwd-PCR-primer-name" "fwd-PCR-primer-seq" "fwd-PCR-primer-seq" "genotype" "genotype" "group" "group" "haplogroup" "haplogroup" "haplotype" "haplotype" "host" "host" "identified-by" "identified-by" "isolate" "isolate" "isolation-source" "isolation-source" "lab-host" "lab-host" "lat-lon" "lat-lon" "linkage-group" "linkage-group" "map" "map" "mating-type" "mating-type" "note" "note" "organism" "organism" "pathovar" "pathovar" "plasmid-name" "plasmid-name" "plastid-name" "plastid-name" "pop-variant" "pop-variant" "rev-PCR-primer-name" "rev-PCR-primer-name" "rev-PCR-primer-seq" "rev-PCR-primer-seq" "segment" "segment" "serogroup" "serogroup" "serotype" "serotype" "serovar" "serovar" "sex" "sex" "specimen-voucher" "specimen-voucher" "strain" "strain" "sub-species" "sub-species" "subclone" "subclone" "subgroup" "subgroup" "substrain" "substrain" "subtype" "subtype" "synonym" "synonym" "teleomorph" "teleomorph" "tissue-lib" "tissue-lib" "tissue-type" "tissue-type" "type" "type" "variety" "variety" var "q5val" type text default "Known bug: Do not use this field." panel var "q6" type chooser default 1 choices "+" " [%Q6FIELD%=%Q6VAL%]" "-" "" var "q6field" type combobox default 42 choices "acronym" "acronym" "altitude" "altitude" "anamorph" "anamorph" "authority" "authority" "bio-material" "bio-material" "biotype" "biotype" "biovar" "biovar" "breed" "breed" "cell-line" "cell-line" "cell-type" "cell-type" "chemovar" "chemovar" "chromosome" "chromosome" "clone" "clone" "clone-lib" "clone-lib" "collected-by" "collected-by" "collection-date" "collection-date" "common" "common" "country" "country" "cultivar" "cultivar" "culture-collection" "culture-collection" "dev-stage" "dev-stage" "ecotype" "ecotype" "endogenous-virus-name" "endogenous-virus-name" "forma" "forma" "forma-specialis" "forma-specialis" "fwd-PCR-primer-name" "fwd-PCR-primer-name" "fwd-PCR-primer-seq" "fwd-PCR-primer-seq" "genotype" "genotype" "group" "group" "haplogroup" "haplogroup" "haplotype" "haplotype" "host" "host" "identified-by" "identified-by" "isolate" "isolate" "isolation-source" "isolation-source" "lab-host" "lab-host" "lat-lon" "lat-lon" "linkage-group" "linkage-group" "map" "map" "mating-type" "mating-type" "note" "note" "organism" "organism" "pathovar" "pathovar" "plasmid-name" "plasmid-name" "plastid-name" "plastid-name" "pop-variant" "pop-variant" "rev-PCR-primer-name" "rev-PCR-primer-name" "rev-PCR-primer-seq" "rev-PCR-primer-seq" "segment" "segment" "serogroup" "serogroup" "serotype" "serotype" "serovar" "serovar" "sex" "sex" "specimen-voucher" "specimen-voucher" "strain" "strain" "sub-species" "sub-species" "subclone" "subclone" "subgroup" "subgroup" "substrain" "substrain" "subtype" "subtype" "synonym" "synonym" "teleomorph" "teleomorph" "tissue-lib" "tissue-lib" "tissue-type" "tissue-type" "type" "type" "variety" "variety" var "q6val" type text default "" panel var "q7" type chooser default 1 choices "+" " [%Q7FIELD%=%Q7VAL%]" "-" "" var "q7field" type combobox default 42 choices "acronym" "acronym" "altitude" "altitude" "anamorph" "anamorph" "authority" "authority" "bio-material" "bio-material" "biotype" "biotype" "biovar" "biovar" "breed" "breed" "cell-line" "cell-line" "cell-type" "cell-type" "chemovar" "chemovar" "chromosome" "chromosome" "clone" "clone" "clone-lib" "clone-lib" "collected-by" "collected-by" "collection-date" "collection-date" "common" "common" "country" "country" "cultivar" "cultivar" "culture-collection" "culture-collection" "dev-stage" "dev-stage" "ecotype" "ecotype" "endogenous-virus-name" "endogenous-virus-name" "forma" "forma" "forma-specialis" "forma-specialis" "fwd-PCR-primer-name" "fwd-PCR-primer-name" "fwd-PCR-primer-seq" "fwd-PCR-primer-seq" "genotype" "genotype" "group" "group" "haplogroup" "haplogroup" "haplotype" "haplotype" "host" "host" "identified-by" "identified-by" "isolate" "isolate" "isolation-source" "isolation-source" "lab-host" "lab-host" "lat-lon" "lat-lon" "linkage-group" "linkage-group" "map" "map" "mating-type" "mating-type" "note" "note" "organism" "organism" "pathovar" "pathovar" "plasmid-name" "plasmid-name" "plastid-name" "plastid-name" "pop-variant" "pop-variant" "rev-PCR-primer-name" "rev-PCR-primer-name" "rev-PCR-primer-seq" "rev-PCR-primer-seq" "segment" "segment" "serogroup" "serogroup" "serotype" "serotype" "serovar" "serovar" "sex" "sex" "specimen-voucher" "specimen-voucher" "strain" "strain" "sub-species" "sub-species" "subclone" "subclone" "subgroup" "subgroup" "substrain" "substrain" "subtype" "subtype" "synonym" "synonym" "teleomorph" "teleomorph" "tissue-lib" "tissue-lib" "tissue-type" "tissue-type" "type" "type" "variety" "variety" var "q7val" type text default "" # - - - - - - - Sequence Properties - - - - - - - tab "Properties" var "seqprops" type chooser label "Sequence Properties" default 0 choices "+" "[mol_type=%MTYPE%] %TOPOLOGY% [location=%LOCATION%] %GERM% %ENV% %META% %REARR% %TRANS% %CODE%" "-" "" # Choices commented out claim to be supported in the documentation, # but don't actually work with tbl2asn. var "mtype" type combobox label "Molecule type" default 0 choices "genomic DNA" "genomic" # "genomic RNA" "genomic rna" # "pre RNA" "pre rna" "mRNA" "mrna" "rRNA" "rrna" "tRNA" "trna" "other genetic" "other genetic" "viral cRNA" "crna" "transcribed RNA" "transcribed rna" # "tmRNA" "tmrna" # "ncrna" "ncrna" var "topology" type chooser label "topology" default 0 choices "linear" "" "circular" "[topology=circular]" var "location" type combobox label "location" default 0 choices "genomic" "genomic" "mitochondrion" "mitochondrion" "chloroplast" "chloroplast" "apicoplast" "apicoplast" "chromatophore" "chromatophore" "chromoplast" "chromoplast" "cyanelle" "cyanelle" "endogenous-virus" "endogenous-virus" "extrachromosomal" "extrachromosomal" "hydrogenosome" "hydrogenosome" "kinetoplast" "kinetoplast" "leucoplast" "leucoplast" "macronuclear" "macronuclear" "nucleomorph" "nucleomorph" "plasmid" "plasmid" "plastid" "plastid" "proplastid" "proplastid" "proviral" "proviral" var "germ" type chooser label "germline" default 1 choices "Yes" "[germline=TRUE]" "No" "" panel var "code" type chooser label "" default 0 choices "genetic code" "[gcode=%GC%]" "mito. genetic code" "[mgcode=%GC%]" var "gc" type combobox label "Genetic code" default 0 choices "Standard Code" "1" "Vertebrate Mitochondrial Code" "2" "Yeast Mitochondrial Code" "3" "Mold, Protozoan, and Coelenterate Mito. and Mycoplasma/Spiroplasma Code" "4" "Invertebrate Mitochondrial Code" "5" "Ciliate, Dasycladacean and Hexamita Nuclear Code" "6" "Echinoderm and Flatworm Mitochondrial Code" "9" "Euplotid Nuclear Code" "10" "Bacterial, Archaeal and Plant Plastid Code" "11" "Alternative Yeast Nuclear Code" "12" "Ascidian Mitochondrial Code" "13" "Alternative Flatworm Mitochondrial Code" "14" "Chlorophycean Mitochondrial Code" "16" "Trematode Mitochondrial Code" "21" "Scenedesmus obliquus Mitochondrial Code" "22" "Thraustochytrium Mitochondrial Code" "23" "Pterobranchia Mitochondrial Code" "24" "Candidate Division SR1 and Gracilibacteria Code" "25" "Pachysolen tannophilus Nuclear Code" "26" "Karyorelict Nuclear" "27" "Condylostoma Nuclear" "28" "Mesodinium Nuclear" "29" "Peritrich Nuclear" "30" "Blastocrithidia Nuclear" "31" var "env" type chooser label "Environmental sample" default 1 choices "Yes" "[environmental-sample=TRUE]" "No" "" var "meta" type chooser label "metagenomic sample" default 1 choices "Yes" "[metagenomic=TRUE]" "No" "" var "rearr" type chooser label "rearranged" default 1 choices "Yes" "[rearranged=TRUE]" "No" "" var "trans" type chooser label "transgenic" default 1 choices "Yes" "[transgenic=TRUE]" "No" "" panel var "Run" type button label "Run" shell "if [ ! -d %RESULTDIR% ]; then mkdir %RESULTDIR%; fi; tbl2asn -p . -t %TEMPLATE% -x %SUFFIX% %COMMENT% -X%XA%%XE% %MASTERGENOME% %RTAX% %LOCALIDS% -a %GAPANNO% -V%VV%%VB%%VR%%VG% -c%CF%%CX%%CD% %ADDITIONAL% -j '%SOURCEQUAL% %SEQPROPS%' -r %RESULTDIR% %SFOUT% -Z %RESULTDIR%/discrepancies.tbl2asn; cd %RESULTDIR%; blreads" # shell "echo %Q6% %Q5% %Q4% [%q4field%=%q4val%]" close true var "Guide" type button label "User Guide" shell "$BIRCH/script/chooseviewer.py http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2" close false var "Manual" type button label "Manual" shell "$BIRCH/script/chooseviewer.py $BIRCH/doc/NCBI/tbl2asn.man" close false