c80b3c968b30abb3f54f63cb50e2aa41bbab5cfd
max
  Tue Aug 18 21:18:10 2015 -0700
adapt spelling and activate mouse overs in extTools menu, refs #15113

diff --git src/hg/hgTracks/extTools.ra src/hg/hgTracks/extTools.ra
index 7095b71..98f155d 100644
--- src/hg/hgTracks/extTools.ra
+++ src/hg/hgTracks/extTools.ra
@@ -1,371 +1,269 @@
+# accepted wildcards:
+# Existing URL replacement chars in trackDb, e.g.
+# $s - chrom name, stripping "chr"
+# $S - full chrom name, leaving "chr"
+# $[ - start position of window
+# $] - end position of window
+# $n - current organism name, spaces replaced with underscores
+# $D - current database, like hg19
+
+# Additional ones:
+# $seq - current sequence in view
+# $taxId - taxon id of current db
+# $returnUrl - full URL of current hgTracks page
+# $position - current position, format chr:start-end
+# $halfLen - 1/2 of the current window size (for pointing external tools to the current center)
+
+# If something doesn't work, Hit "Esc" when the redirection takes place and append 
+# &debug=1
+# to the URL shown in the browser (it has hgt.redirectTool=xxx in it)
+# This will show all parameters sent to the external site and lets you edit them.
+
+tool NCBIPrev
+shortLabel NCBI Map Viewer
+longLabel NCBI Genome Browser
+url http://www.ncbi.nlm.nih.gov/mapview/maps.cgi
+email info@ncbi.nlm.nih.gov
+onlyDbs hg19
+isHttpGet true
+param taxId $taxId
+param CHR $s
+param BEG $[
+param END $]
+param build previous
+
 tool NCBI
 shortLabel NCBI Map Viewer
-longLabel NCBI MapViewer Genome Browser
-url http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=$taxId&build=previous&CHR=$s&BEG=$[&END=$]
-# for which DBS?
-#dbs hg19
+longLabel NCBI Genome Browser
+url http://www.ncbi.nlm.nih.gov/mapview/maps.cgi
+email info@ncbi.nlm.nih.gov
+notDbs hg19
+isHttpGet true
+param taxId $taxId
+param CHR $s
+param BEG $[
+param END $]
+
+tool ensemblArch
+shortLabel Ensembl
+longLabel Ensembl Genome Browser
+url http://dec2014.archive.ensembl.org/$n/contigview
+onlyDbs hg38
+email helpdesk@ensembl.org
+isHttpGet true
+param chr $s
+param start $[
+param end $]
 
 tool ensembl
 shortLabel Ensembl
 longLabel Ensembl Genome Browser
-url http://www.ensembl.org/$n/contigview?chr=$s&start=$[&end=$]
-# for which DBs?
-#dbs hg19
+url http://www.ensembl.org/$n/contigview
+email helpdesk@ensembl.org
+notDbs hg38
+isHttpGet true
+param chr $s
+param start $[
+param end $]
 
 tool primer3Plus
 shortLabel Primer3Plus
-longLabel Updated version of the well-known primer designer
-url http://primer3plus.ut.ee/cgi-bin/primer3plus/primer3plus.cgi
-maxSize 8000
-param SEQUENCE_INTERNAL_EXCLUDED_REGION
-param PRIMER_SALT_DIVALENT 1.5
-param PRIMER_WT_SELF_ANY 0.0
-param PRIMER_FIRST_BASE_INDEX 1
-param PRIMER_INSIDE_PENALTY -1.0
-param PRIMER_MAX_SELF_ANY 8.00
-param PRIMER_WT_TM_GT 1.0
-param PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT 1
-param PRIMER_INTERNAL_WT_SELF_ANY_TH 0.0
-param PRIMER_WT_TM_LT 1.0
-param PRIMER_INTERNAL_WT_HAIRPIN_TH 0.0
-param PRIMER_MAX_SELF_END 3.00
-param PRIMER_PICK_ANYWAY 1
-param PRIMER_MAX_LIBRARY_MISPRIMING 12.00
-param PRIMER_TASK generic
-param PRIMER_PRODUCT_SIZE_RANGE 150-250 100-300 301-400 401-500 501-600 601-700 701-850 851-1000
-param PRIMER_PAIR_WT_COMPL_ANY_TH 0.0
-param PRIMER_MAX_POLY_X 4
-param PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE 3
-param PRIMER_WT_NUM_NS 0.0
-param PRIMER_INTERNAL_MAX_LIBRARY_MISHYB 12.00
-param PRIMER_PAIR_WT_PRODUCT_TM_LT 0.0
-param PRIMER_MAX_TEMPLATE_MISPRIMING_TH 40.00
-param PRIMER_MAX_HAIRPIN_TH 24.00
-param PRIMER_SALT_CORRECTIONS 1
-param PRIMER_INTERNAL_MAX_SELF_ANY 12.00
-param PRIMER_WT_POS_PENALTY 0.0
-param PRIMER_INTERNAL_MIN_SIZE 18
-param PRIMER_OUTSIDE_PENALTY 0.0
-param PRIMER_SEQUENCING_LEAD 50
-param PRIMER_MIN_RIGHT_THREE_PRIME_DISTANCE 3
-param PRIMER_WT_GC_PERCENT_GT 0.0
-param PRIMER_LIBERAL_BASE 1
-param PRIMER_MIN_QUALITY 0
-param PRIMER_WT_TEMPLATE_MISPRIMING 0.0
-param PRIMER_INTERNAL_WT_TM_LT 1.0
-param PRIMER_WT_TEMPLATE_MISPRIMING_TH 0.0
-param PRIMER_TM_FORMULA 1
-param PRIMER_SEQUENCING_ACCURACY 20
-param SEQUENCE_START_CODON_POSITION 
-param PRIMER_OPT_SIZE 20
-param PRIMER_MIN_TM 57.0
-param SEQUENCE_PRIMER_REVCOMP 
-param PRIMER_PAIR_WT_IO_PENALTY 0.0
-param PRIMER_INTERNAL_DNTP_CONC 0.0
-param PRIMER_QUALITY_RANGE_MIN 0
-param PRIMER_MIN_5_PRIME_OVERLAP_OF_JUNCTION 7
-param SEQUENCE_QUALITY 
-param PRIMER_PAIR_WT_PRODUCT_SIZE_LT 0.0
-param SEQUENCE_FORCE_LEFT_END 
-param PRIMER_INTERNAL_WT_SIZE_LT 1.0
-param PRIMER_MUST_MATCH_FIVE_PRIME 
-param PRIMER_WT_SEQ_QUAL 0.0
-param PRIMER_INTERNAL_OPT_GC_PERCENT 50.0
-param PRIMER_PAIR_WT_COMPL_ANY 0.0
-param SEQUENCE_FORCE_LEFT_START 
-param PRIMER_PICK_LEFT_PRIMER 1
-param PRIMER_NUM_RETURN 5
-param PRIMER_PRODUCT_MAX_TM 1000000.0
-param PRIMER_MIN_END_QUALITY 0
-param PRIMER_DNTP_CONC 0.6
-param PRIMER_PRODUCT_MIN_TM -1000000.0
-param PRIMER_INTERNAL_MUST_MATCH_THREE_PRIME 
-param SEQUENCE_ID 
-param PRIMER_DNA_CONC 50.0
-param PRIMER_SALT_MONOVALENT 50.0
-param PRIMER_INTERNAL_MISHYB_LIBRARY NONE
-param PRIMER_INTERNAL_SALT_MONOVALENT 50.0
-param PRIMER_INTERNAL_MAX_SIZE 27
-param PRIMER_OPT_TM 59.0
-param PRIMER_INTERNAL_OPT_SIZE 20
-param PRIMER_WT_SELF_END 0.0
-param PRIMER_PAIR_WT_COMPL_END 0.0
-param PRIMER_MIN_SIZE 18
-param PRIMER_INTERNAL_MIN_GC 20.0
-param PRIMER_QUALITY_RANGE_MAX 100
-param PRIMER_INTERNAL_WT_SELF_END_TH 0.0
-param SEQUENCE_PRIMER_PAIR_OK_REGION_LIST 
-param PRIMER_PAIR_WT_TEMPLATE_MISPRIMING_TH 0.0
-param PRIMER_INTERNAL_MUST_MATCH_FIVE_PRIME 
-param PRIMER_MAX_TEMPLATE_MISPRIMING 12.00
-param PRIMER_INTERNAL_WT_SEQ_QUAL 0.0
-param SEQUENCE_TARGET $halfLen,1
-param PRIMER_INTERNAL_MIN_QUALITY 0
-param PRIMER_WT_END_STABILITY 0.0
-param PRIMER_INTERNAL_WT_END_QUAL 0.0
-param PRIMER_INTERNAL_MAX_HAIRPIN_TH 47.00
-param PRIMER_MIN_GC 30.0
-param PRIMER_INTERNAL_DNA_CONC 50.0
-param PRIMER_INTERNAL_WT_SELF_ANY 0.0
-param PRIMER_PAIR_MAX_LIBRARY_MISPRIMING 20.00
-param PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING_TH 70.00
-param SCRIPT_PRODUCT_MAX_SIZE 
-param PRIMER_INTERNAL_MAX_POLY_X 5
-param PRIMER_OPT_GC_PERCENT 50.0
-param SCRIPT_PRODUCT_MIN_SIZE 
-param PRIMER_WT_SELF_ANY_TH 0.0
-param PRIMER_WT_SIZE_GT 1.0
-param PRIMER_PAIR_WT_DIFF_TM 0.0
-param PRIMER_PICK_RIGHT_PRIMER 1
-param PRIMER_PAIR_WT_PRODUCT_TM_GT 0.0
-param PRIMER_INTERNAL_WT_GC_PERCENT_GT 0.0
-param PRIMER_PAIR_MAX_COMPL_END 3.00
-param PRIMER_PAIR_MAX_DIFF_TM 5.0
-param PRIMER_INTERNAL_WT_LIBRARY_MISHYB 0.0
-param PRIMER_WT_SELF_END_TH 0.0
-param PRIMER_MAX_GC 80.0
-param PRIMER_PAIR_WT_TEMPLATE_MISPRIMING 0.0
-param PRIMER_MAX_NS_ACCEPTED 0
-param SCRIPT_RADIO_BUTTONS_FIX PRIMER_PICK_LEFT_PRIMER,PRIMER_PICK_INTERNAL_OLIGO,PRIMER_PICK_RIGHT_PRIMER,PRIMER_PICK_ANYWAY,PRIMER_LIBERAL_BASE,PRIMER_LOWERCASE_MASKING,PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS,PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT,PRIMER_THERMODYNAMIC_TEMPLATE_ALIGNMENT,SCRIPT_DISPLAY_DEBUG_INFORMATION
-param PRIMER_INTERNAL_WT_TM_GT 1.0
-param P3P_PRIMER_NAME_ACRONYM_RIGHT R
-param PRIMER_PAIR_WT_PRODUCT_SIZE_GT 0.0
-param PRIMER_WT_LIBRARY_MISPRIMING 0.0
-param PRIMER_PAIR_WT_PR_PENALTY 1.0
-param PRIMER_SEQUENCING_INTERVAL 250
-param PRIMER_PRODUCT_OPT_SIZE 
-param PRIMER_WT_END_QUAL 0.0
-param P3P_PRIMER_NAME_ACRONYM_SPACER _
-param PRIMER_GC_CLAMP 0
-param PRIMER_MAX_END_STABILITY 9.0
-param PRIMER_MUST_MATCH_THREE_PRIME 
-param SEQUENCE_FORCE_RIGHT_START 
-param PRIMER_MAX_SELF_ANY_TH 45.00
-param PRIMER_MAX_SELF_END_TH 35.00
-param PRIMER_INTERNAL_MAX_GC 70.0
-param SEQUENCE_PRIMER 
-param PRIMER_INTERNAL_WT_GC_PERCENT_LT 0.0
-param SEQUENCE_EXCLUDED_REGION 
-param SCRIPT_SERVER_PARAMETER_FILE Default
-param PRIMER_INTERNAL_MAX_SELF_END 12.00
-param PRIMER_INTERNAL_MAX_NS_ACCEPTED 0
-param PRIMER_PAIR_MAX_COMPL_ANY 8.00
-param P3P_PRIMER_NAME_ACRONYM_LEFT F
-param PRIMER_MISPRIMING_LIBRARY NONE
-param PRIMER_MAX_SIZE 23
-param SCRIPT_SEQUENCE_FILE 
-param SEQUENCE_INCLUDED_REGION 
-param PRIMER_INTERNAL_OPT_TM 60.0
-param PRIMER_PAIR_MAX_COMPL_END_TH 35.00
-param PRIMER_INTERNAL_MAX_SELF_END_TH 47.00
-param SEQUENCE_FORCE_RIGHT_END 
-param PRIMER_PAIR_MAX_COMPL_ANY_TH 45.00
-param PRIMER_WT_GC_PERCENT_LT 0.0
+longLabel Updated interface of the popular primer designer. Primers flank the nucleotide in the center of the screen.
+url http://primer3plus.com/cgi-bin/geneBro/primer3plus.cgi
+email server@untergasser.de
+maxSize 10000
+param GENBRO_RETURN_PATH $returnUrl
+param GENBRO_DB $db
+param GENBRO_POSITION $position
 param SEQUENCE_TEMPLATE $seq
-param PRIMER_MAX_TM 62.0
-param PRIMER_INTERNAL_WT_NUM_NS 0.0
-param PRIMER_INTERNAL_MIN_TM 57.0
-param PRIMER_SEQUENCING_SPACING 500
-param P3P_PRIMER_NAME_ACRONYM_INTERNAL IN
-param PRIMER_PAIR_WT_LIBRARY_MISPRIMING 0.0
-param PRIMER_INTERNAL_WT_SELF_END 0.0
-param PRIMER_WT_SIZE_LT 1.0
-param PRIMER_INTERNAL_WT_SIZE_GT 1.0
-param PRIMER_MAX_END_GC 5
-param PRIMER_INTERNAL_MAX_SELF_ANY_TH 47.00
-param SEQUENCE_OVERLAP_JUNCTION_LIST 
-param Pick_Primers Pick Primers
-param PRIMER_PRODUCT_OPT_TM 0.0
-param PRIMER_MIN_3_PRIME_OVERLAP_OF_JUNCTION 4
-param PRIMER_INTERNAL_MAX_TM 63.0
-param SEQUENCE_INTERNAL_OLIGO 
-param SCRIPT_SETTINGS_FILE 
-param PRIMER_INTERNAL_SALT_DIVALENT 1.5
-param PRIMER_WT_HAIRPIN_TH 0.0
-param PRIMER_PAIR_WT_COMPL_END_TH 0.0
-param PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING 24.00
 
 tool RnaFold
-shortLabel RnaFold
+shortLabel RNAfold
 longLabel RNA secondary structure prediction
 url http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi
+email rna@tbi.univie.ac.at
 maxSize 5000
 param SHAPEFILE 
 param reliability on
 param shape_beta 0.8
 param FILE 
 param EMAIL your e-mail
 param SHAPEDATA 
 param mountain on
 param Temp 37
 param shape_conv_linearlog_s 1.6
 param CONSTRAINT 
 param shapemethod deigan
 param param rna2004
 param shape_slope 1.9
 param shape_conv_linearlog_i -2.29
 param method p
 param shape_conv_linear_i 0.2
 param deigan_conversion linearlog
 param dangling d2
 param SCREEN $seq
 param shape_conv_linear_s 0.68
 param proceed 
 param svg on
 param noLP on
 param shape_conv_cutoff 0.25
 param shape_intercept -0.7
 param PAGE 2
 
 tool rsatMeta
 shortLabel RSAT Metazoa
 longLabel Regulatory Sequence Analysis Tools for Metazoa
 url http://rsat.sb-roscoff.fr/convert-seq.cgi 
+email Jacques.van-Helden@univ-amu.fr
 maxSize 50000
 param short_size 30 
 param line_width 60 
 param sequence $seq
 param output_format fasta 
 param mask non-dna 
 param .cgifields addrcoutput 
 param .submit GO 
 param short_action no treatment 
 param sequence_format raw 
 param output display 
 param uploaded_file  
 param user_email  
 
 tool promoter2
 shortLabel Promoter 2
 longLabel Vertebrate Transcription Start Site Prediction
 url http://www.cbs.dtu.dk/cgi-bin/webface2.fcgi
+email rapacki@cbs.dtu.dk
 maxSize 50000
 param configfile /usr/opt/www/pub/CBS/services/Promoter-2.0/Promoter.cf
 param SEQPASTE $seq
 param SEQSUB 
 
 tool uniprobe
 shortLabel Uniprobe
 longLabel Search for transcription factor binding sites
 url http://the_brain.bwh.harvard.edu/uniprobe/browse.php
-maxSize 200
+email uniprobe@genetics.med.harvard.edu
+maxSize 80
 param MAX_FILE_SIZE 2097152
 param dnaSpeciesFormat all
 param dnaThreshold 0.45
 param dnaSpeciesTextArea             
 param dnaSpeciesSingle Acanthamoeba castellanii
 param dnaTextarea $seq
 param searchParam 
 param dnaSpeciesCategory Acanthamoeba castellanii,Allomyces macrogynus,Ashbya gossypii,Arabidopsis thaliana,Aspergillus nidulans,Caenorhabditis elegans,Cryptosporidium parvum,Drosophila melanogaster,Homo sapiens,Kluyveromyces lactis,Monosiga brevicollis,Mus musculus,Mycosphaerella graminicola,Nematostella vectensis,Patiria miniata,Plasmodium falciparum,Saccharomyces cerevisiae,Strongylocentrotus purpuratus,Trichoplax adhaerens,Tuber melanosporum
 param dnaFile 
 param dnaFormat textarea
 
 tool primerBlast
 shortLabel Primer-BLAST
-longLabel Primer3-based primer designer that checks matches via NCBI BLAST
+longLabel Primer3-based primer designer that also checks matches via NCBI BLAST
 url http://www.ncbi.nlm.nih.gov/tools/primer-blast/primertool.cgi
+email info@ncbi.nlm.nih.gov
 maxSize 50000
 param EXCLUDED_REGIONS 
 param PRIMER_INTERNAL_OLIGO_MAX_GC 80.0
 param LOW_COMPLEXITY_FILTER on
 param SELF_ANY 8.00
 param SALT_FORMULAR 1
 param PRIMER_INTERNAL_OLIGO_OPT_TM 60.0
 param PRIMER_INTERNAL_OLIGO_MIN_SIZE 18
 param PRIMER_NUM_RETURN 10
 param OVERLAP_3END 4
 param HITSIZE 50000
 param PRIMER_PAIR_MAX_COMPL_ANY_TH 45.0
 param PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT 50
 param PRIMER_MAX_HAIRPIN_TH 24.0
 param SEARCHMODE 0
 param TM_METHOD 1
 param SEARCH_SPECIFIC_PRIMER on
 param EVALUE 30000
 param SELF_END 3.00
 param TOTAL_MISMATCH_IGNORE 6
 param DIVA_CATIONS 1.5
 param PRIMER_SPECIFICITY_DATABASE refseq_mrna
 param MAX_TARGET_PER_TEMPLATE 100
 param PRIMER5_START 
 param MAX_TARGET_SIZE 4000
 param CMD request
 param PRIMER_OPT_SIZE 20
 param PRIMER_MIN_TM 57.0
 param MAX_INTRON_SIZE 1000000
 param UNGAPPED_BLAST on
 param MIN_INTRON_SIZE 1000
 param PRIMER_INTERNAL_OLIGO_MAX_SIZE 27
 param PRIMER_MAX_END_GC 5
 param PRIMER3_START 
 param ORG_DBS 
 param PRIMER5_END 
 param OVERLAP_5END 7
 param PRIMER_PRODUCT_MIN 70
 param SPLICE_SITE_OVERLAP_3END 4
 param SVIEWER_DATA_KEY 
 param INPUT_SEQUENCE $seq
 param NUM_TARGETS_WITH_PRIMERS 1000
 param PRIMER_PRODUCT_MAX 1000
 param PRIMER_3END_SPECIFICITY_MISMATCH 1
 param SHOW_SVIEWER onon
 param PRIMER_OPT_TM 60.0
 param PRIMER_MIN_SIZE 15
 param NUM_DIFFS 0
 param ORGANISM Homo%20sapiens
 param PRIMER_MAX_TEMPLATE_MISPRIMING 12.00
 param MONO_CATIONS 50.0
 param PRIMER_MIN_GC 20.0
 param PRODUCT_OPT_TM 
 param PRIMER_ON_SPLICE_SITE 0
 param MISMATCH_REGION_LENGTH 5
 param PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING_TH 70.00
 param PRIMER_MAX_SELF_ANY_TH 45.0
 param PRIMER_INTERNAL_OLIGO_MAX_TM 63.0
 param slctOrg 
 param CON_ANEAL_OLIGO 50.0
 param PRIMER_PAIR_MAX_COMPL_END 3.00
 param ENTREZ_QUERY 
 param PRIMER_MAX_GC 80.0
 param SEQFILE 
 param SPLICE_SITE_OVERLAP_5END 7
 param OVERLAP 
 param PRIMER_MAX_END_STABILITY 9
 param WORD_SIZE 7
 param PRODUCT_MAX_TM 
 param PRIMER_INTERNAL_OLIGO_MIN_TM 57.0
 param TOTAL_PRIMER_SPECIFICITY_MISMATCH 1
 param CON_DNTPS 0.6
 param PRIMER_MAX_SELF_END_TH 35.0
 param NUM_TARGETS 20
 param CUSTOMSEQFILE 
 param PRIMER_PAIR_MAX_COMPL_ANY 8.00
 param PRIMER_MISPRIMING_LIBRARY AUTO
 param PRIMER_MAX_SIZE 25
 param PRIMER_RIGHT_INPUT 
 param PRIMER_PAIR_MAX_COMPL_END_TH 35.0
 param LINK_LOC 
 param PRIMER_INTERNAL_OLIGO_OPT_SIZE 20
 param PRIMER_LEFT_INPUT 
 param PRODUCT_MIN_TM 
 param PRIMER_MAX_TEMPLATE_MISPRIMING_TH 40.00
 param PRIMER_MAX_TM 63.0
 param PRIMER3_END 
 param POLYX 5
 param PRIMER_INTERNAL_OLIGO_MIN_GC 20.0
 param NUM_OPTS_DIFFS 0
 param GC_CLAMP 0
 param PRIMER_MAX_DIFF_TM 3
 param MAX_CANDIDATE_PRIMER 500
 param CUSTOM_DB 
 param PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING 24.00
 
 tool crispor
 url http://tefor.net/crisporMax/crispor.cgi
+email services@tefor.net
 shortLabel CRISPOR
 longLabel CRISPR/Cas9 target selector and offtarget-predictor
 param org $db
 param pos $position
 param pam NGG
-maxSize 2000
+maxSize 1000