73064807840ba9f4cdc2e6e71b945a502de5190e
max
  Fri Aug 21 07:54:13 2015 -0700
adding external tool regrna2, refs #15113

diff --git src/hg/hgTracks/extTools.ra src/hg/hgTracks/extTools.ra
index 41d0054..aefe656 100644
--- src/hg/hgTracks/extTools.ra
+++ src/hg/hgTracks/extTools.ra
@@ -123,31 +123,31 @@
 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
+longLabel Regulatory Sequence Analysis Tools for Metazoa. Can search for Transcription Factor binding sites and over-represented words.
 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  
@@ -311,15 +311,61 @@
 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
+
+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