cd042ca8342c4278e51a558b1968f26949a7458d max Fri Nov 13 15:00:40 2015 -0800 adding crispor back to external tools and sending them info they need to build custom tracks, refs #16308 diff --git src/hg/hgTracks/extTools.ra src/hg/hgTracks/extTools.ra index 8bc4025..1d299bb 100644 --- src/hg/hgTracks/extTools.ra +++ src/hg/hgTracks/extTools.ra @@ -166,53 +166,59 @@ 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 @@ -235,30 +241,33 @@ 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/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 @@ -268,56 +277,63 @@ 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 $start1 +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 words. +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 @@ -328,39 +344,39 @@ #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/crisporMax/crispor.cgi -#email services@tefor.net -#shortLabel CRISPOR -#longLabel CRISPR/Cas9 target selector: off-target and activity predictions, primer design -#param org $db -#param pos $position -#param pam NGG -#maxSize 1000 +tool crispor +url http://tefor.net/crispor/crispor.cgi +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 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 2000 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 @@ -370,15 +386,19 @@ 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 +onlyDbs hg19,hg38,ce10,dm3,mm10,oryLat2,rn5,sacCer3,xenTro3,galGal4