# DO NOT EDIT THIS FILE! # This file is automatically generated by blastdbkit.py during installation, # update or by birchadmin --> UpdateAddInstall name "BLASTX - trans. DNA vs local protein database" icon "$BIRCH/pkg/NCBI/NCBI_tiny.png" tip "trans. DNA vs. local protein database" var "in1" type tempfile direction in format fasta save true tabset # - - - - - - - - - - - - - - - - - - - - - - - tab "General search options" var "dbase" type combobox label "Database" default 0 choices @include $BIRCH/local/admin/BLAST/BLASTDB.pro.blinclude "User-created BLAST database" "-db `echo %USERFILE% | sed 's/\(.*\)\..*/\1/'`" "User-created file (FASTA format)" "-subject %USERFILE%" var "userfile" type file label "filename" var "searchtask" type combobox label "Type of search" default 1 choices "blastx" "blastx" "blastx-fast, faster, optimized for >= 50% identity" "blastx-fast" var "gencode" type combobox label "Genetic Code" default 0 choices "Standard" "1" "Vertebrate Mitochondrial" "2" "Yeast Mitochondrial" "3" "Mold, Protozoan, and Coelenterate Mitochondrial" "4" "Invertebrate Mitochondrial" "5" "Ciliate, Dasycladacean and Hexamita" "6" "Echinoderm and Flatworm" "9" "Euplotid" "10" "Bacterial and Plant Plastid" "11" "Alternative Yeast Nuclear" "12" "Ascidian Mitochondrial" "13" "Alternative Flatworm Mitochondrial" "14" "Blepharisma" "15" "Chlorophycean Mitochondrial" "16" "Trematode Mitochondrial" "21" "Scenedesmus obliquus mitochondrial" "22" "Thraustochytrium Mitochondrial" "23" var "evalue" type combobox label "E: # matches expected by random chance" default 0 choices "1.0e-11" "1.0e-11" "1.0e-10" "1.0e-10" "1.0e-9" "1.0e-9" "1.0e-8" "1.0e-8" "1.0e-7" "1.0e-7" "1.0e-6" "1.0e-6" "1.0e-5" "1.0e-5" "0.0001" "0.0001" "0.001" "0.001" "0.01" "0.01" "0.1" "0.1" "1" "1" "10" "10" "100" "100" var "threads" type number label "Number of threads to use" min 1 max $BL_CORES_MAX default $BL_CORES_DEFAULT # - - - - - - - - - - - - - - - - - - - - - - - tab "Query filtering" var "strand" type chooser label "Strand(s)" default 0 choices "Both strands" "-strand both" "Plus strand" "-strand plus" "Minus strand" "-strand minus" var "seg" type chooser label "Filter out low complexity regions with SEG" default 1 choices "yes" "-seg yes" "no" "" var "smask" type chooser label "Mask for lookup table only" default 1 choices "yes" "-soft_masking true" "no" "" var "lmask" type chooser label "Mask letters from input that are lowercase" default 1 choices "yes" "-lcase_masking" "no" "" # - - - - - - - - - - - - - - - - - - - - - - - tab "Restrict search" var "oquery" type combobox label "ORGANISM:" default 2 choices "Only search these organisms" "-entrez_query '%OSTRING% [orgn]'" "Search all EXCEPT these organisms" "-entrez_query 'NOT %OSTRING% [orgn]'" "All" "" var "ostring" type text label "common name, binomial or taxid" default "none" var "equery" type chooser label "Restrict search to entries containing string:" default 1 choices "Yes" "-entrez_query '%ESTRING%'" "No" "" var "estring" type text label "Entrez query string" default "none" # - - - - - - - - - - - - - - - - - - - - - - - tab "Scoring" var "matrix" type combobox label "SCORING MATRIX" default 1 choices "Blosum45 (Protein)" "BLOSUM45" "Blosum62 (Protein default)" "BLOSUM62" "Blosum80 (Protein)" "BLOSUM80" "PAM30 (Protein)" "PAM30" "PAM70 (Protein)" "PAM70" var "word" type chooser label "Word size" default 1 choices "2" "-word_size 2" "3" "-word_size 3" "6" "-word_size 6" var "gapped" type chooser label "Perform gapped alignment?" default 0 choices "Yes" "" "No" "-ungapped" # BLAST has a limited set of open/extend penalties for each scoring matrix. # For example, the ones below are valid for BLOSUM62, but not BLOSUM45. # It won't run if you don't give a valid pair of penalties. # Until we can get some sort of if/then logic into PCD, this var should # be commented out, and we just let BLAST choose gap penalties # var "gap" # type combobox # label "Gap penalties" # default 6 # choices # "Open: 9 Extend: 2" "-gapopen 9 -gapextend 2" # "Open: 8 Extend: 2" "-gapopen 8 -gapextend 2" # "Open: 7 Extend: 2" "-gapopen 7 -gapextend 2" # "Open: 6 Extend: 2" "-gapopen 6 -gapextend 2" # "Open: 5 Extend: 2" "-gapopen 5 -gapextend 2" # "Open: 12 Extend: 1" "-gapopen 12 -gapextend 1" # "Open: 11 Extend: 1" "-gapopen 11 -gapextend 1" # "Open: 10 Extend: 1" "-gapopen 10 -gapextend 1" # "Open: 9 Extend: 1" "-gapopen 9 -gapextend 1" # "Open: 8 Extend: 1" "-gapopen 8 -gapextend 1" # - - - - - - - - - - - - - - - - - - - - - - - tab "Output" var "voptions" type combobox label "Alignment view options" default 0 choices "pairwise" "0" "query-anchored showing identities" "1" "query-anchored no identities" "2" "flat query-anchored, show identities" "3" "flat query-anchored, no identities" "4" "XML Blast output" "5" "tabular" "6" "tabular with comment lines" "7" "Text ASN.1" "8" "Binary ASN.1" "9" "CSV - comma-separated values" "10" "BLAST archive format (ASN.1)" "11" "Seqalign (JSON)" "12" "Multiple-file BLAST JSON" "13" "Multiple-file BLAST XML2" "14" "Single-file BLAST JSON" "15" "Single-file BLAST XML2" "16" # SAM only applicable for DNA to DNA comparisons #"Sequence Alignment/Map (SAM)" "17" "Organism Report" "18" var "maxdisp" type combobox label "Max. num. of alignments to display" default 4 choices "10" "10" "50" "50" "100" "100" "250" "250" "500" "500" "1000" "1000" "5000" "5000" "10000" "10000" "20000" "20000" var "writereport" type combobox label "WHERE TO SEND BLAST REPORT" default 1 choices "none" "" "Web Browser" "blblastout.py --archive %in1%.blastx.asn1 --destination browser --outfmt %VOPTIONS%;" "Text Editor" "blblastout.py --archive %in1%.blastx.asn1 --destination textedit --outfmt %VOPTIONS%;" "HTML file" "blblastout.py --archive %in1%.blastx.asn1 --destination htmlfile --outfmt %VOPTIONS% --outfile %OUTNAME%;" "Text file" "blblastout.py --archive %in1%.blastx.asn1 --destination textfile --outfmt %VOPTIONS% --outfile %OUTNAME%;" var "writetsv" type combobox label "WHERE TO SEND TABLE OF HITS" default 1 choices "none" "" "blpfetch" "blblastout.py --archive %in1%.blastx.asn1 --destination blpfetch --outfmt 7,sacc,stitle,sscinames,staxids,evalue,length,slen,mismatch,gapopen,qstart,qend,sstart,send,bitscore,pident;" "tsvfile" "blblastout.py --archive %in1%.blastx.asn1 --destination tsvfile --outfmt 7,sacc,stitle,sscinames,staxids,evalue,length,slen,mismatch,gapopen,qstart,qend,sstart,send,bitscore,pident --outfile %OUTNAME%;" var "writexml" type combobox label "WHERE TO SEND XML OUTPUT" default 1 choices "none" "" "BlastViewer" "blblastout.py --archive %in1%.blastx.asn1 --destination blastviewer --outfmt 5;" "xmlfile" "blblastout.py --archive %in1%.blastx.asn1 --destination xmlfile --outfmt 5 --outfile %OUTNAME%;" var "outname" type text label " Base name for output files" var "email" type chooser label "Notify of completion by email" default 1 choices "Yes" "echo 'Query: '`grep '>' %in1%` > %in1%.log; echo 'Database: '%DBASE% >> %in1%.log; bl_email.py --recipient %ADDRESS% --subject 'blastx completed' --message %in1%.log; rm %in1%.log;" "No" "" var "address" type text label " email address" default "$BL_EMAIL" panel var "Run" type button label "Run" shell "(nice -n 4 blastx -query %in1% %DBASE% -task %SEARCHTASK% -query_gencode %GENCODE% -evalue %EVALUE% -num_threads %THREADS% %STRAND% %SEG% %SMASK% %LMASK% %OQUERY% %EQUERY% -matrix %MATRIX% %WORD% %GAPPED% -outfmt 11 -max_target_seqs %MAXDISP% -show_gis -parse_deflines -out %in1%.blastx.asn1; %WRITEREPORT% %WRITETSV% %WRITEXML% %EMAIL% rm -f %in1% %in1%.blastx.asn1)&" close true var "Help" type button label "Help" shell "chooseviewer.py $BIRCH/doc/NCBI/blastx.txt" close false