# HG changeset patch
# User bjoern-gruening
# Date 1326279452 18000
# Node ID b46d3df3eb9ef396b6241f10cedeede6f9f8aae1
Initial commit
diff -r 000000000000 -r b46d3df3eb9e readme.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.txt Wed Jan 11 05:57:32 2012 -0500
@@ -0,0 +1,80 @@
+Galaxy wrapper for t-RNA prediction tools
+=========================================
+
+This wrapper is copyright 2012 by Björn Grüning.
+
+This prepository contains wrapper for the command line tools of tRNAscan-SE and Arogorn.
+http://lowelab.ucsc.edu/tRNAscan-SE/
+http://130.235.46.10/ARAGORN/
+
+
+Dean Laslett and Bjorn Canback
+ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences Nucl. Acids Res. (2004) 32(1): 11-16
+doi:10.1093/nar/gkh152
+
+Todd M. Lowe and Sean R. Eddy
+tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Nucl. Acids Res. (1997) 25(5): 0955-964
+doi:10.1093/nar/25.5.0955
+
+
+
+Installation
+============
+
+Please download tRNAscan-SE from the following URL and follow the install instructions.
+
+http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz
+
+Arogorn can be download from:
+
+http://mbio-serv2.mbioekol.lu.se/ARAGORN/aragorn1.2.33.c
+With a recent GNU-Compiler (gcc) you can compile it with the following command.
+
+gcc -O3 -ffast-math -finline-functions -o aragorn aragorn1.2.33.c
+
+Please include aragorn and tRNAscan-SE into your PATH.
+export PATH=$PATH:/home/user/bin/aragorn/bin/
+
+
+To install the wrappers copy the files aragorn.xml and tRNAscan.xml in the galaxy tools
+folder and modify the tools_conf.xml file to make the tool available to Galaxy.
+For example add the following lines:
+
+
+
+
+
+
+History
+=======
+
+tRNAscan:
+v0.1 - Initial public release
+
+aragorn:
+v0.1 - Initial public release
+
+
+
+
+Wrapper Licence (MIT/BSD style)
+===============================
+
+Permission to use, copy, modify, and distribute this software and its
+documentation with or without modifications and for any purpose and
+without fee is hereby granted, provided that any copyright notices
+appear in all copies and that both those copyright notices and this
+permission notice appear in supporting documentation, and that the
+names of the contributors or copyright holders not be used in
+advertising or publicity pertaining to distribution of the software
+without specific prior permission.
+
+THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
+WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
+OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
+OR PERFORMANCE OF THIS SOFTWARE.
+
diff -r 000000000000 -r b46d3df3eb9e tool_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_conf.xml Wed Jan 11 05:57:32 2012 -0500
@@ -0,0 +1,7 @@
+
+
+
+
+
+
+
diff -r 000000000000 -r b46d3df3eb9e tools/aragorn.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/aragorn.xml Wed Jan 11 05:57:32 2012 -0500
@@ -0,0 +1,124 @@
+
+ Prediction of tRNAs
+ aragorn $input > $output
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+This tool predicts, tRNA (and tmRNA) detection in nucleotide sequences.
+http://130.235.46.10/ARAGORN/
+-----
+
+**Example**
+
+Suppose you have the following DNA formatted sequences::
+
+ >SQ Sequence 8667507 BP; 1203558 A; 3121252 C; 3129638 G; 1213059 T; 0 other;
+ cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
+ ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
+ cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
+ cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
+ ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg
+
+Running this tool will produce this::
+ --snip--
+ 87.
+
+ c
+ c
+ a
+ g-c
+ g-c
+ g-c
+ c-g
+ g-c
+ a-t
+ t-a ca
+ t tgacc a
+ ga a !!!!! g
+ t ctcg actgg c
+ g !!!! c tt
+ g gagc t
+ aa g g
+ c-gag
+ t-a
+ t-a
+ c-g
+ g-c
+ t c
+ t a
+ cac
+
+
+
+ tRNA-Val(cac)
+ 74 bases, %GC = 58.1
+ Sequence [6669703,6669776]
+
+
+
+
+ tRNA Anticodon Frequency
+ AAA Phe GAA Phe 1 CAA Leu 1 TAA Leu 1
+ AGA Ser GGA Ser 1 CGA Ser 2 TGA Ser 1
+ ACA Cys GCA Cys 2 CCA Trp 2 TCA seC
+ ATA Tyr GTA Tyr 1 CTA Pyl TTA Stop
+ AAG Leu GAG Leu 3 CAG Leu 1 TAG Leu 2
+ AGG Pro GGG Pro 2 CGG Pro 2 TGG Pro 2
+ ACG Arg 1 GCG Arg 2 CCG Arg 1 TCG Arg
+ ATG His GTG His 2 CTG Gln 2 TTG Gln 1
+ AAC Val GAC Val 3 CAC Val 2 TAC Val 1
+ AGC Ala GGC Ala 2 CGC Ala 3 TGC Ala 1
+ ACC Gly GCC Gly 5 CCC Gly 1 TCC Gly 2
+ ATC Asp GTC Asp 3 CTC Glu 2 TTC Glu 2
+ AAT Ile GAT Ile 3 CAT Met 6 TAT Ile
+ AGT Thr GGT Thr 2 CGT Thr 1 TGT Thr 2
+ ACT Ser GCT Ser 1 CCT Arg 1 TCT Arg 1
+ ATT Asn GTT Asn 3 CTT Lys 3 TTT Lys 2
+ Ambiguous: 1
+
+ tRNA Codon Frequency
+ TTT Phe TTC Phe 1 TTG Leu 1 TTA Leu 1
+ TCT Ser TCC Ser 1 TCG Ser 2 TCA Ser 1
+ TGT Cys TGC Cys 2 TGG Trp 2 TGA seC
+ TAT Tyr TAC Tyr 1 TAG Pyl TAA Stop
+ CTT Leu CTC Leu 3 CTG Leu 1 CTA Leu 2
+ CCT Pro CCC Pro 2 CCG Pro 2 CCA Pro 2
+ CGT Arg 1 CGC Arg 2 CGG Arg 1 CGA Arg
+ CAT His CAC His 2 CAG Gln 2 CAA Gln 1
+ GTT Val GTC Val 3 GTG Val 2 GTA Val 1
+ GCT Ala GCC Ala 2 GCG Ala 3 GCA Ala 1
+ GGT Gly GGC Gly 5 GGG Gly 1 GGA Gly 2
+ GAT Asp GAC Asp 3 GAG Glu 2 GAA Glu 2
+ ATT Ile ATC Ile 3 ATG Met 6 ATA Ile
+ ACT Thr ACC Thr 2 ACG Thr 1 ACA Thr 2
+ AGT Ser AGC Ser 1 AGG Arg 1 AGA Arg 1
+ AAT Asn AAC Asn 3 AAG Lys 3 AAA Lys 2
+ Ambiguous: 1
+
+ Number of tRNA genes = 86
+ tRNA GC range = 50.0% to 85.1%
+ Number of tmRNA genes = 1
+
+-------
+
+**References**
+
+Dean Laslett and Bjorn Canback
+ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences Nucl. Acids Res. (2004) 32(1): 11-16
+doi:10.1093/nar/gkh152
+
+
+
+
+
diff -r 000000000000 -r b46d3df3eb9e tools/tRNAscan.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/tRNAscan.xml Wed Jan 11 05:57:32 2012 -0500
@@ -0,0 +1,214 @@
+
+ tRNA Scan
+ tRNAscan-SE $organism $mode $showPrimSecondOpt $disablePseudo $showCodons -d -Q -y -q -b -o $output $inputfile > /dev/null
+
+
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+.. class:: warningmark
+
+**TIP** This tool requires *fasta* format.
+
+-----
+
+**What it does**
+
+ tRNAscan-SE was designed to make rapid, sensitive searches of genomic
+ sequence feasible using the selectivity of the Cove analysis package.
+ We have optimized search sensitivity with eukaryote cytoplasmic and
+ eubacterial sequences, but it may be applied more broadly with a
+ slight reduction in sensitivity .
+ http://lowelab.ucsc.edu/tRNAscan-SE/
+
+-----
+
+**Organisim**
+
+- use general tRNA model:
+
+ This option selects the general tRNA covariance model that was trained
+ on tRNAs from all three phylogenetic domains (archaea, bacteria, and
+ eukarya). This mode can be used when analyzing a mixed collection of
+ sequences from more than one phylogenetic domain, with only slight
+ loss of sensitivity and selectivity. The original publication
+ describing this program and tRNAscan-SE version 1.0 used this general
+ tRNA model exclusively. If you wish to compare scores to those found
+ in the paper or scans using v1.0, use this option. Use of this option
+ is compatible with all other search mode options described in this
+ section.
+
+- search for bacterial tRNAs
+
+ This option selects the bacterial covariace model for tRNA analysis,
+ and loosens the search parameters for EufindtRNA to improve detection
+ of bacterial tRNAs. Use of this mode with bacterial sequences
+ will also improve bounds prediction of the 3' end (the terminal CAA
+ triplet).
+
+- search for archaeal tRNAs
+
+ This option selects an archaeal-specific covariance model for tRNA
+ analysis, as well as slightly loosening the EufindtRNA search
+ cutoffs.
+
+- search for organellar (mitochondrial/chloroplast) tRNAs
+
+ This parameter bypasses the fast first-pass scanners that are poor at
+ detecting organellar tRNAs and runs Cove analysis only. Since true
+ organellar tRNAs have been found to have Cove scores between 15 and 20
+ bits, the search cutoff is lowered from 20 to 15 bits. Also,
+ pseudogene checking is disabled since it is only applicable to
+ eukaryotic cytoplasmic tRNA pseudogenes. Since Cove-only mode is
+ used, searches will be very slow (see -C option below) relative to the
+ default mode.
+
+------
+
+**Mode**
+
+- search using Cove analysis only (max sensitivity, slow)
+
+ Directs tRNAscan-SE to analyze sequences using Cove analysis only.
+ This option allows a slightly more sensitive search than the default
+ tRNAscan + EufindtRNA -> Cove mode, but is much slower (by approx. 250
+ to 3,000 fold). Output format and other program defaults are
+ otherwise identical to the normal analysis.
+
+- search using Eukaryotic tRNA finder (EufindtRNA) only:
+
+ This option runs EufindtRNA alone to search for tRNAs. Since Cove is
+ not being used as a secondary filter to remove false positives, this
+ run mode defaults to "Normal" parameters which more closely
+ approximates the sensitivity and selectivity of the original algorithm
+ describe by Pavesi and colleagues.
+
+- search using tRNAscan only (defaults to strict search params)
+
+ Directs tRNAscan-SE to use only tRNAscan to analyze sequences. This
+ mode will cause tRNAscan to default to using "strict" parameters
+ (similar to tRNAscan version 1.3 operation). This mode of operation
+ is faster (about 3-5 times faster than default mode analysis), but
+ will result in approximately 0.2 to 0.6 false positive tRNAs per Mbp,
+ decreased sensitivity, and less reliable prediction of anticodons,
+ tRNA isotype, and introns.
+
+-----
+
+**disable pseudogene checking**
+
+ Manually disable checking tRNAs for poor primary or secondary
+ structure scores often indicative of eukaryotic pseudogenes. This
+ will slightly speed the program and may be necessary for non-eukaryotic
+ sequences that are flagged as possible pseudogenes but are known to be
+ functional tRNAs.
+
+-----
+
+**Show both primary and secondary structure score components to covariance model bit scores**
+
+ This option displays the breakdown of the two components of the
+ covariance model bit score. Since tRNA pseudogenes often have one
+ very low component (good secondary structure but poor primary sequence
+ similarity to the tRNA model, or vice versa), this information may be
+ useful in deciding whether a low-scoring tRNA is likely to be a
+ pseudogene. The heuristic pseudogene detection filter uses this
+ information to flag possible pseudogenes -- use this option to see why
+ a hit is marked as a possible pseudogene. The user may wish to
+ examine score breakdowns from known tRNAs in the organism of interest
+ to get a frame of reference.
+
+-----
+
+**Show codons instead of tRNA anticodons**
+
+ This option causes tRNAscan-SE to output a tRNA's corresponding codon
+ in place of its anticodon.
+
+-----
+
+**Example**
+
+* input::
+
+ -Genome Sequence
+
+ CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7
+ GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
+ GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
+ TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
+ TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
+ GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
+ ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
+ AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
+ CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA
+ TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC
+ AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA
+ GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC
+ AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC
+ CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA
+ AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC
+ GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT
+ .....
+ - organisim : Mixed (general tRNA model)
+ - mode : Default
+ - disable pseudogene checking : not checked
+ - Show both primary and secondary structure score components to covariance model bit scores : not checked
+ - Show codons instead of tRNA anticodons : not checked
+
+* output::
+
+ Sequence tRNA Bounds tRNA Anti Intron Bounds Cove Hit
+ Name tRNA # Begin End Type Codon Begin End Score Origin
+ -------- ------ ---- ------ ---- ----- ----- ---- ------ ------
+ CELF22B7 1 12619 12738 Leu CAA 12657 12692 55.12 Bo
+ CELF22B7 2 19480 19561 Ser AGA 0 0 66.90 Bo
+ CELF22B7 3 26367 26439 Phe GAA 0 0 73.88 Bo
+ CELF22B7 4 26992 26920 Phe GAA 0 0 73.88 Bo
+ CELF22B7 5 23765 23694 Pro CGG 0 0 60.58 Bo
+
+
+
+-------
+
+**References**
+
+Todd M. Lowe and Sean R. Eddy
+tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Nucl. Acids Res. (1997) 25(5): 0955-964
+doi:10.1093/nar/25.5.0955
+
+
+
+