# HG changeset patch
# User bjoern-gruening
# Date 1331736016 14400
# Node ID 9fb7ae02453cca1fe91238d39dc686a4fbdc4695
initial uploaded
diff -r 000000000000 -r 9fb7ae02453c augustus/augustus.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/augustus/augustus.xml Wed Mar 14 10:40:16 2012 -0400
@@ -0,0 +1,180 @@
+
+ gen prediction for eukaryotic genomes
+ augustus
+ --strand=$strand
+ $noInFrameStop
+ $gff
+ $protein
+ $introns
+ $start
+ $stop
+ $cds
+ $codingseq
+ $singlestrand
+ $input_genome
+ --genemodel=$genemodel
+ --species=$organism
+ --outfile=$output
+
+ #please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
+ #or use the --AUGUSTUS_CONFIG_PATH=path switch
+
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+ augustus
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+**What it does**
+
+AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller.
+It can be used as an ab initio program, which means it bases its prediction purely on the
+sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources
+such as EST, MS/MS, protein alignments and synthenic genomic alignments.
+
+-----
+
+**Parameters**
+
+Gene Model::
+
+ partial : allow prediction of incomplete genes at the sequence boundaries (default)
+ intronless : only predict single-exon genes like in prokaryotes and some eukaryotes
+ complete : only predict complete genes
+ atleastone : predict at least one complete gene
+ exactlyone : predict exactly one complete gene
+
+
+
+**Example**
+
+Suppose you have the following DNA formatted sequences::
+
+ >Seq1
+ cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
+ ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
+ cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
+ cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
+ ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg
+
+Running this tool will produce this::
+
+ # ----- prediction on sequence number 1 (length = 1992969, name = scaffold1|size1992969) -----
+ #
+ # Constraints/Hints:
+ # (none)
+ # Predicted genes for sequence number 1 on both strands
+ # start gene g1
+ scaffold1|size1992969 AUGUSTUS gene 17453 19382 0.11 + . g6
+ scaffold1|size1992969 AUGUSTUS transcript 17453 19382 0.11 + . g6.t1
+ scaffold1|size1992969 AUGUSTUS start_codon 17453 17455 . + 0 transcript_id "g6.t1"; gene_id "g6";
+ scaffold1|size1992969 AUGUSTUS intron 17615 17660 0.38 + . transcript_id "g6.t1"; gene_id "g6";
+ scaffold1|size1992969 AUGUSTUS intron 17708 17772 0.54 + . transcript_id "g6.t1"; gene_id "g6";
+ scaffold1|size1992969 AUGUSTUS intron 17902 18035 0.58 + . transcript_id "g6.t1"; gene_id "g6";
+ scaffold1|size1992969 AUGUSTUS intron 18313 18367 0.99 + . transcript_id "g6.t1"; gene_id "g6";
+ scaffold1|size1992969 AUGUSTUS intron 19014 19080 0.44 + . transcript_id "g6.t1"; gene_id "g6";
+ scaffold1|size1992969 AUGUSTUS CDS 17453 17614 0.55 + 0 transcript_id "g6.t1"; gene_id "g6";
+ scaffold1|size1992969 AUGUSTUS CDS 17661 17707 0.38 + 0 transcript_id "g6.t1"; gene_id "g6";
+ scaffold1|size1992969 AUGUSTUS CDS 17773 17901 0.54 + 1 transcript_id "g6.t1"; gene_id "g6";
+ scaffold1|size1992969 AUGUSTUS CDS 18036 18312 0.52 + 1 transcript_id "g6.t1"; gene_id "g6";
+ scaffold1|size1992969 AUGUSTUS CDS 18368 19013 0.99 + 0 transcript_id "g6.t1"; gene_id "g6";
+ scaffold1|size1992969 AUGUSTUS CDS 19081 19379 0.31 + 2 transcript_id "g6.t1"; gene_id "g6";
+ scaffold1|size1992969 AUGUSTUS stop_codon 19380 19382 . + 0 transcript_id "g6.t1"; gene_id "g6";
+
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diff -r 000000000000 -r 9fb7ae02453c augustus/readme.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/augustus/readme.txt Wed Mar 14 10:40:16 2012 -0400
@@ -0,0 +1,78 @@
+Galaxy wrapper for Augustus
+=====================================
+
+This wrapper is copyright 2012 by Björn Grüning.
+
+This is a wrapper for the command line tool of augustus.
+http://bioinf.uni-greifswald.de/augustus/
+
+AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
+
+Oliver Keller, Martin Kollmar, Mario Stanke, Stephan Waack (2011)
+A novel hybrid gene prediction method employing protein multiple sequence alignments
+Bioinformatics, doi: 10.1093/bioinformatics/btr010
+
+Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008)
+Using native and syntenically mapped cDNA alignments to improve de novo gene finding
+Bioinformatics, doi: 10.1093/bioinformatics/btn013
+
+Mario Stanke and Stephan Waack (2003)
+Gene Prediction with a Hidden-Markov Model and a new Intron Submodel.
+Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225
+
+
+
+
+Installation
+============
+
+Install or downlaod augustus from:
+
+http://bioinf.uni-greifswald.de/augustus/binaries/
+
+and follow the installation instructions or copy the binaries into your $PATH
+
+To install the wrapper copy the augustus folder in the galaxy tools
+folder and modify the tools_conf.xml file to make the tool available to Galaxy.
+For example:
+
+
+
+
+
+
+Set the AUGUSTUS_CONFIG_PATH to /path_to_augustus/augustus/config with
+ export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
+or modify the wrapper and use the following additional commandline switch:
+ --AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
+
+
+
+
+History
+=======
+
+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 9fb7ae02453c augustus/tool_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/augustus/tool_conf.xml Wed Mar 14 10:40:16 2012 -0400
@@ -0,0 +1,6 @@
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