bc3cd36606b2cad0e7fa2b051856397b1c0fdb04 max Thu Sep 21 11:16:29 2017 -0700 fixing crispor external tools entry, must have been broken by some update they did diff --git src/hg/hgTracks/extTools.ra src/hg/hgTracks/extTools.ra index 2052b0e..92f8ce2 100644 --- src/hg/hgTracks/extTools.ra +++ src/hg/hgTracks/extTools.ra @@ -1,408 +1,408 @@ # 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 # $start1 - start position of window + 1 # $] - 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. # Note that these configuration entries do not have to be created manually # We have a tool "extToolsChromeParse" that can parse the Chrome debug # trace to create them automatically from a traced click on a link in Chrome # Run the tool "extToolsChromeParse" and look at its help message for details tool NCBIPrev shortLabel NCBI Map Viewer longLabel NCBI Genome Browser url https://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 $start1 param END $] param build previous tool NCBI shortLabel NCBI Map Viewer longLabel NCBI Genome Browser url https://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 $start1 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 $start1 param end $] tool ensembl shortLabel Ensembl longLabel Ensembl Genome Browser url http://www.ensembl.org/$n/contigview email helpdesk@ensembl.org notDbs hg38 isHttpGet true param chr $s param start $start1 param end $] tool primer3Plus shortLabel Primer3Plus longLabel Updated interface of the popular primer designer. Primers flank the nucleotide in the center of the screen. url http://primer3plus.com/cgi-bin/dev/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 tool primerBlast shortLabel Primer-BLAST longLabel Primer3-based primer designer that also checks matches via NCBI BLAST url https://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 param chrom $s param start $[ param db $db tool nebcutter shortLabel NEBCutter longLabel New England Biolabs Restriction Enzyme Site Predictor (Note: the Browser also has a track with restriction sites.) #email NEEDTOFILLOUT maxSize 300000 url http://nc2.neb.com/NEBcutter2/enzcut.php param no_dam 0 param add_type13 0 param add_nick 0 param sequence $seq param no_ecobi 0 param seqisfrag 0 param no_ecoki 0 param no_dcm 0 param no_cpg 0 param cut_to 0 param gcode 11 param min_orf 100 param cut_from 0 param circular 0 param add_homing 0 param enz_suppl 1 param chrom $s param start $[ param db $db tool regrna2 shortLabel RegRNA 2 longLabel Predicts pre-mRNA motifs, polyadenylation sites, splicing motifs, Ribosome binding sites, UTR motifs, RNA editing sites, Riboswitches, RNA regulatory elements and miRNA and ncRNA target sites email kevinchang1025@gmail.com url http://regrna2.mbc.nctu.edu.tw/detection_output.php onlyDbs hg17,hg18,hg19,hg38 maxSize 2000 param GeneSplicer_species Human param position_line_interval_len 100 param S1 $faSeq param UTRsite ON param ncRNA_FE -20 param SplicingMotif ON param Rfam ON param RBSfinder ON param ERPIN ON param ncRNA ON param fRNAdb ON param StartCodon 1 param draw_dotline ON param score 170 param matchscore 1 param SplicingSite ON param GCratio_window_size 100 param RadioGroup1 matrix param unpair_size 6 param uploadfile param SplicingMotif_species Homo sapiens param miRNA ON param ncRNA_length 20 param Polya ON param miRNA_species Homo sapiens param tfbs_species human, Homo sapiens param RNAediting ON param miRNA_FE -25 param ncRNA_species Homo_sapiens param LongStem ON param fRNAdb_match_len 30 param fRNAdb_similarity 0.9 param B1 Submit param AUrich ON param accessibility_window_size 100 param LongStem_len 40 param RiboSW ON param Size 950 param chrom $s param start $[ param db $db tool RnaFold shortLabel RNAfold longLabel RNA secondary structure prediction url http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/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 param chrom $s param start $[ param db $db tool pfam shortLabel PFAM Search longLabel Annotation of protein domains by the EBI Pfam database email pfam-help@ebi.ac.uk url http://pfam.xfam.org/search/sequence param submit Submit param seq $seq maxSize 80000 param chrom $s param start $[ param db $db 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 # these trigger error messages #param chrom $s #param start $[ #param db $db tool rsatMeta shortLabel RSAT Metazoa longLabel Regulatory Sequence Analysis Tools for Metazoa. Can search for Transcription Factor binding sites and over-represented oligo-nucleotides. 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 ## removed after request from Martha Bulyk. They plan to make their matrix search faster #tool uniprobe #shortLabel Uniprobe #longLabel Search for transcription factor binding sites #url http://the_brain.bwh.harvard.edu/uniprobe/browse.php #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 crispor -url http://tefor.net/crispor/crispor.cgi +url http://crispor.tefor.net/crispor.py email services@tefor.net shortLabel CRISPOR longLabel CRISPR/Cas9 target selector: off-target, activity predictions and primer design param org $db param pos $position param pam NGG maxSize 1000 -onlyDbs hg19,hg38,ce10,dm3,mm10,oryLat2,rn5,sacCer3,xenTro3,galGal4,danRer7,danRer10 +onlyDbs hg19,hg38,ce10,dm3,mm10,oryLat2,rn5,rn6,sacCer3,xenTro3,galGal4,galGal5,danRer7,danRer10,ci2,ci3,equCab2,gasAcu1,loPe1,musFur1,oryLat2,panTro4,papAnu2,rheMac2 tool chopchop url https://chopchop.rc.fas.harvard.edu/search.php email tessa.montague@gmail.com shortLabel CHOPCHOP longLabel CRISPR/Cas9 off-target predictions maxSize 1000 onlyDbs anoGam1,ce10,dm3,hg19,hg38,danRer7,galGal4,gasAcu1,mm10,musFur1,rn6,oryLat2,sacCer3,xenTro3 param organism $db param pasteSeq $seq param position $position param method CRISPR param target CODING param subsetExon param padding param enzyme N param minResSite 4 param searchMethod hsu param 5prime GN,NG param PAM NGG param TALEdist param TALEsize param mismatches 2 param gRVD NN param PRODUCT_SIZE_MIN 150 param PRODUCT_SIZE_MAX 290 param PRIMER_MIN_SIZE 18 param PRIMER_MAX_SIZE 25 param PRIMER_OPT_SIZE 22 param PRIMER_MIN_TM 57 param PRIMER_MAX_TM 63 param PRIMER_OPT_TM 60 param sitePadding 20 param chrom $s param start $[ param db $db