7976e2588e92dca0567231cf3998759bf6f1827f max Thu May 7 03:27:42 2015 -0700 implementing the external tools "send to" menu, refs #15113 diff --git src/hg/hgTracks/extTools.ra src/hg/hgTracks/extTools.ra new file mode 100644 index 0000000..7095b71 --- /dev/null +++ src/hg/hgTracks/extTools.ra @@ -0,0 +1,371 @@ +tool NCBI +shortLabel NCBI MapViewer +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 + +tool ensembl +shortLabel Ensembl +longLabel Ensembl Genome Browser +url http://www.ensembl.org/$n/contigview?chr=$s&start=$[&end=$] +# for which DBs? +#dbs hg19 + +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 +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 +longLabel RNA secondary structure prediction +url http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi +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 +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 Promoter2 +longLabel Vertebrate Transcription Start Site Prediction +url http://www.cbs.dtu.dk/cgi-bin/webface2.fcgi +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 +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 +url http://www.ncbi.nlm.nih.gov/tools/primer-blast/primertool.cgi +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 +shortLabel CRISPOR +longLabel CRISPR/Cas9 target selector and offtarget-predictor +param org $db +param pos $position +param pam NGG +maxSize 2000 +