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changeset 5:a4fab0c1ae1a

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Uploaded
author bjoern-gruening
date Sun, 09 Jun 2013 07:54:25 -0400
parents 796814f16b12
children e664f2137b03
files augustus.xml extract_features.py readme.rst readme.txt test-data/arabidopsis_augustus.fa test-data/arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf test-data/human_augustus.fa test-data/human_augustus_protein_codingseq_introns_cds_codingseq.fasta test-data/human_augustus_protein_codingseq_introns_cds_main.gtf test-data/human_augustus_protein_codingseq_introns_cds_protein.fasta test-data/human_augustus_utr-on.gff test-data/human_augustus_utr-on.gtf tool_dependencies.xml
diffstat 13 files changed, 933 insertions(+), 128 deletions(-) [+]
line wrap: on
line diff
--- a/augustus.xml	Tue Oct 30 06:29:50 2012 -0400
+++ b/augustus.xml	Sun Jun 09 07:54:25 2013 -0400
@@ -1,40 +1,48 @@
-<tool id="augustus" name="Augustus" version="0.2">
-	<description>gene prediction for eukaryotic genomes</description>
+<tool id="augustus" name="Augustus" version="0.3">
+    <description>gene prediction for eukaryotic genomes</description>
     <requirements>
-        <requirement type="package" version="2.6.1">augustus</requirement>
+        <requirement type="package" version="2.7">augustus</requirement>
+        <requirement type="set_environment">AUGUSTUS_SCRIPT_PATH</requirement>
     </requirements>
-    <command>augustus
-        --strand=$strand
-        $noInFrameStop
-        $gff
-        $protein
-        $introns
-        $start
-        $stop
-        $cds
-        $codingseq
-        $singlestrand
-        $input_genome 
-        --genemodel=$genemodel
-        --species=$organism
-        --outfile=$output
+    <command>
+        ## please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
+        ## or use the --AUGUSTUS_CONFIG_PATH=path if you are not installing through the toolshed
+        ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external script is used to extract the sequences into additional files
 
-        #please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
-        #or use the --AUGUSTUS_CONFIG_PATH=path switch
-
+        augustus
+            --strand=$strand
+            $noInFrameStop
+            $gff
+            $protein
+            $introns
+            $start
+            $stop
+            $cds
+            $codingseq
+            $singlestrand
+            $input_genome
+            $mea
+            $utr
+            --genemodel=$genemodel
+            --species=$organism
+            ##--outfile=$output
+        | tee $output 
+        #if $protein or $codingseq:
+            | python \$AUGUSTUS_SCRIPT_PATH/extract_features.py
+                #if $protein:
+                    --protein $protein_output
+                #end if
+                #if $codingseq:
+                    --codingseq $codingseq_output
+                #end if
+        #end if
     </command>
-	<inputs>
-		<param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>
-		<param name="noInFrameStop" type="boolean" label="Don't report transcripts with in-frame stop codons. Otherwise, intron-spanning stop codons could occur" truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false" />
-		<param name="gff" type="boolean" label="GFF formated output, standard is GTF" truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
-		<param name="protein" type="boolean" label="Output predicted protein sequences" truevalue="--protein=on" falsevalue="--protein=off" checked="false" />
-		<param name="introns" type="boolean" label="Output predicted intron sequences" truevalue="--introns=on" falsevalue="--introns=off" checked="false" />
-		<param name="start" type="boolean" label="Output predicted start codons" truevalue="--start=on" falsevalue="--start=off" checked="false" />
-		<param name="stop" type="boolean" label="Output predicted stop codons" truevalue="--stop=on" falsevalue="--stop=off" checked="false" />
-		<param name="cds" type="boolean" label="Output CDS region" truevalue="--cds=on" falsevalue="--cds=off" checked="true" />
-		<param name="codingseq" type="boolean" label="Output coding sequence as comment in the output file" truevalue="--codingseq=on" falsevalue="--codingseq=off" checked="false" />
-
-		<param name="singlestrand" type="boolean" label="Predict genes independently on each strand, allow overlapping genes on opposite strands" truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" />
+    <inputs>
+        <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>
+        <param name="noInFrameStop" type="boolean" label="Don't report transcripts with in-frame stop codons (--noInFrameStop)" truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false" help="Otherwise, intron-spanning stop codons could occur" />
+        <param name="singlestrand" type="boolean" label="Predict genes independently on each strand, allow overlapping genes on opposite strands (--singlestrand)" truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" />
+        <param name="mea" type="boolean" label="Using the maximum expected accuracy approach (--mea)" truevalue="--mea=1" falsevalue="" checked="false" help="MEA is an alternative decoding approach." />
+        <param name="utr" type="boolean" label="Predict the untranslated regions in addition to the coding sequence (--UTR)" truevalue="--UTR=on" falsevalue="--UTR=off" checked="false" help="This currently works only for human, galdieria, toxoplasma and caenorhabditis." />
 
         <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
             <option value="human">Homo sapiens</option>
@@ -42,7 +50,7 @@
             <option value="arabidopsis">Arabidopsis thaliana</option>
             <option value="brugia ">Brugia malayi</option>
             <option value="aedes">Aedes aegypti</option>
-            <option value="tribolium">Tribolium castaneum</option>
+            <option value="tribolium2012">Tribolium castaneum</option>
             <option value="schistosoma">Schistosoma mansoni</option>
             <option value="tetrahymena">Tetrahymena thermophila</option>
             <option value="galdieria">Galdieria sulphuraria</option>
@@ -88,10 +96,14 @@
             <option value="ustilago_maydis">Ustilago maydis</option>
             <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
             <option value="nasonia">Nasonia vitripennis</option>
-            <option value="tomato ">Solanum lycopersicum</option>
+            <option value="tomato">Solanum lycopersicum</option>
             <option value="chlamydomonas">Chlamydomonas reinhardtii</option>
-            <option value="amphimedon ">Amphimedon queenslandica</option>
-            <option value="pneumocystis ">Pneumocystis jirovecii</option>
+            <option value="amphimedon">Amphimedon queenslandica</option>
+            <option value="pneumocystis">Pneumocystis jirovecii</option>
+            <option value="chicken">Gallus gallus domesticus (chicken)</option>
+            <option value="cacao">Theobroma cacao (cacao)</option>
+            <option value="heliconius_melpomene1">Heliconius melpomene</option>
+            <option value="xenoturbella">Xenoturbella</option>
         </param> 
 
         <param name="strand" type="select" multiple="false" format="text" help="Report predicted genes on both strands, just the forward or just the backward strand.">
@@ -106,16 +118,64 @@
             <option value="intronless">intronless</option>
             <option value="atleastone">atleastone</option>
             <option value="exactlyone">exactlyone</option>
+            <option value="bacterium">bacterium (beta version)</option>
         </param>
 
-	</inputs>
-	<outputs>
+        <param name="protein" type="boolean" label="Output predicted protein sequences (--protein)" truevalue="--protein=on" falsevalue="--protein=off" checked="true" />
+        <param name="codingseq" type="boolean" label="Output coding sequence as comment in the output file (codingseq)" truevalue="--codingseq=on" falsevalue="--codingseq=off" checked="true" />
+        <param name="introns" type="boolean" label="Output predicted intron sequences (--introns)" truevalue="--introns=on" falsevalue="--introns=off" checked="false" />
+        <param name="start" type="boolean" label="Output predicted start codons (--start)" truevalue="--start=on" falsevalue="--start=off" checked="false" />
+        <param name="stop" type="boolean" label="Output predicted stop codons (--stop)" truevalue="--stop=on" falsevalue="--stop=off" checked="false" />
+        <param name="cds" type="boolean" label="Output CDS region (--cds)" truevalue="--cds=on" falsevalue="--cds=off" checked="true" />
+        <param name="gff" type="boolean" label="GFF formated output, standard is GTF (--gff3)" truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
+
+    </inputs>
+    <outputs>
         <data format="gtf" name="output">
             <change_format>
                 <when input="gff" value="--gff3=on" format="gff" />
             </change_format>
         </data>
+        <data format="fasta" name="protein_output">
+            <filter>protein == True</filter>
+        </data>
+        <data format="fasta" name="codingseq_output">
+            <filter>codingseq == True</filter>
+        </data>
     </outputs>
+    <tests>
+        <test>
+            <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
+            <param name="organism" value="human" />
+            <param name="utr" value="--UTR=on" />
+            <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="2"/>
+        </test>
+        <test>
+            <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
+            <param name="organism" value="human" />
+            <param name="utr" value="--UTR=on" />
+            <param name="gff" value="--gff3=on" />
+            <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="2"/>
+        </test>
+        <test>
+            <param name="input_genome" value="arabidopsis_augustus.fa" ftype="fasta" />
+            <param name="organism" value="arabidopsis" />
+            <param name="singlestrand" value="--singlestrand=true" />
+            <param name="mea" value="--mea=1" />
+            <output name="output" file="arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf" ftype="gtf" lines_diff="2"/>
+        </test>
+        <test>
+            <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
+            <param name="organism" value="human" />
+            <param name="protein" value="--protein=on" />
+            <param name="codingseq" value="--codingseq=on" />
+            <param name="introns" value="--introns=on" />
+            <param name="cds" value="--cds=on" />
+            <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gff" lines_diff="2"/>
+            <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" />
+            <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />
+        </test>
+    </tests>
     <help>
 
 **What it does**
@@ -125,7 +185,7 @@
 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**
 
@@ -182,5 +242,5 @@
 Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225
 
 
-	</help>
+    </help>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_features.py	Sun Jun 09 07:54:25 2013 -0400
@@ -0,0 +1,93 @@
+#!/usr/bin/env python
+
+import os
+import sys
+import argparse
+import textwrap
+
+def main( args ):
+    """
+    Extract the protein and coding section from an augustus gff, gtf file
+    Example file:
+HS04636	AUGUSTUS	stop_codon	6901	6903	.	+	0	Parent=g1.t1
+HS04636	AUGUSTUS	transcription_end_site	8857	8857	.	+	.	Parent=g1.t1
+# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
+# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
+# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
+# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
+# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
+# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
+# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
+# end gene g1
+###
+#
+# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
+#
+# Predicted genes for sequence number 2 on both strands
+# start gene g2
+HS08198	AUGUSTUS	gene	86	2344	1	+	.	ID=g2
+HS08198	AUGUSTUS	transcript	86	2344	.	+	.	ID=g2.t1;Parent=g2
+HS08198	AUGUSTUS	transcription_start_site	86	86	.	+	.	Parent=g2.t1
+HS08198	AUGUSTUS	exon	86	582	.	+	.	Parent=g2.t1
+HS08198	AUGUSTUS	start_codon	445	447	.	+	0	Parent=g2.t1
+    """
+    protein_seq = ''
+    coding_seq = ''
+    if args.protein:
+        po = open( args.protein, 'w+' )
+    if args.codingseq:
+        co = open( args.codingseq, 'w+' )
+
+    for line in sys.stdin:
+        # protein- and coding-sequence are stored as comments
+        if line.startswith('#'):
+            line = line[2:].strip()
+            if line.startswith('start gene'):
+                gene_name = line[11:].strip()
+
+            if args.protein and line.startswith('protein sequence = ['):
+                if line.endswith(']'):
+                    protein_seq = line[20:-1]
+                    po.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) )
+                    protein_seq = ''
+                else:
+                    line = line[20:]
+                    protein_seq = line
+
+            if args.codingseq and line.startswith('coding sequence = ['):
+                if line.endswith(']'):
+                    coding_seq = line[19:-1]
+                    co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) )
+                    coding_seq = ''
+                else:
+                    line = line[19:]
+                    coding_seq = line
+
+            if protein_seq:
+                if line.endswith(']'):
+                    protein_seq += line[:-1]
+                    po.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) )
+                    protein_seq = ''
+                else:
+                    protein_seq += line
+
+            if coding_seq:
+                if line.endswith(']'):
+                    coding_seq += line[:-1]
+                    co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) )
+                    coding_seq = ''
+                else:
+                    coding_seq += line
+    if args.codingseq:
+        co.close()
+    if args.protein:
+        po.close()
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-p', '--protein', help='Path to the protein file.')
+    parser.add_argument('-c', '--codingseq', help='Path to the coding file.')
+
+    args = parser.parse_args()
+    main( args )
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Sun Jun 09 07:54:25 2013 -0400
@@ -0,0 +1,83 @@
+Galaxy wrapper for Augustus
+===========================
+
+This wrapper is copyright 2012-2013 by Björn Grüning.
+
+This is a wrapper for the command line tool of Augustus_.
+
+.. _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
+============
+
+The recommended installation is by means of the toolshed_.
+If you need to install it manually here is a short introduction.
+
+.. _toolshed: http://toolshed.g2.bx.psu.edu/view/bjoern-gruening/augustus
+
+
+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::
+
+  <section name="Gene Prediction" id="gene_prediction">
+    <tool file="gene_prediction/tools/augustus/augustus.xml" />
+  </section>
+
+
+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
+- v0.2: Added tool_dependencies.xml file and update the augustus version (thanks to James Johnson)
+- v0.3: upgrade to augustus 2.7, added new organisms and new parameters, output additional sequence files
+
+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.
+
--- a/readme.txt	Tue Oct 30 06:29:50 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
-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:
-
-<section name="Gene Prediction" id="gene_prediction">
-    <tool file="gene_prediction/tools/augustus/augustus.xml" />
-</section>
-
-
-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
-v0.2 - Added tool_dependencies.xml file and update the augustus version (thanks to James Johnson)
-
-
-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.
-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/arabidopsis_augustus.fa	Sun Jun 09 07:54:25 2013 -0400
@@ -0,0 +1,53 @@
+>arabidopsis
+ATATCATTCATGGGCCCCTACGCATTACTCGGTACCAATCTCGCTCTCTCTCTCTAAGTCTTGAAACTCTATCAAGAAT
+CTCAAGCCACCATTTTTTCTTCATCTTCATAAAGAGAAAGAGAGAGATCCTCTTGTTTGGCAAGAACCCAATTTGAGTT
+CTAAGTCCTGATTTGCTTAGCTCTTTTCTTTCCTTGATTTCATTCTATATAAAGTCAACGGAAAGATATACATATATAG
+TTTTCTTCCGATTCTAGGGTTTTCATATTTCCTCTAAATTTTCATGGTCAAAGAAGAAAATCTAAGAAACAATCGAACC
+AGCAAGAGAAAGAAGACTTCAATATCAACATCTCTCTCTCCCTCTCTCTCTCTTATATTATAAGGTGAGACCACAAGAA
+CTTTTGATTTTCTTTTTCCTTCTTCCCTTCTTTTAATATATTCTTTGAATTTTTTTTCACTAATTCATCTACCCTTTTT
+TATAATTGTGGCTAGATTTTTGTTTCGTTTCCTCTTTTTAATATTATCTCTCTAATGTATGTTGAAGATCTCGAGTTGA
+GTCATCATCATCGTCAATGGCTTTGAAAAACATCCGCAACAATTCACCAATTGAAGAACAAGAGAAAGGTTTAAACTTC
+ATCAAGATTCACTAAGACCCACTAAGAGCCAACTCAAAACTAAACGGAGCAAGGTTTTGCCAAAAACCAAAAAAAAAAA
+AAAAAAGATTCAAGAACCATCTCGTAAATCAAGATTTCTCCAAGGAAAATCAGATAAGTCATAATGGATCTATCCCTGG
+CTCCGACAACAACAACAAGTTCCGACCAAGAACAAGACAGAGACCAAGAATTAACCTCCAACATCGGAGCAAGCAGCAG
+CTCCGGTCCCAGCGGAAACAACAACAACCTTCCGATGATGATGATTCCACCTCCGGAGAAAGAACACATGTTCGACAAA
+GTGGTAACACCAAGCGACGTCGGAAAACTCAACAGACTCGTGATCCCTAAACAACACGCTGAGAGGTATTTCCCTCTAG
+ACTCCTCAAACAACCAAAACGGCACGCTTTTGAACTTCCAAGACAGAAACGGCAAGATGTGGAGATTCCGTTACTCGTA
+TTGGAACTCTAGCCAGAGCTACGTTATGACCAAAGGATGGAGCCGTTTCGTCAAAGAGAAAAAGCTCGATGCAGGAGAC
+ATTGTCTCTTTCCAACGAGGCATCGGAGATGAGTCAGAAAGATCCAAACTTTACATAGATTGGAGGCATAGACCCGACA
+TGAGCCTCGTTCAAGCACATCAGTTTGGTAATTTTGGTTTCAATTTCAATTTCCCGACCACTTCTCAATATTCCAACAG
+ATTTCATCCATTGCCAGAATATAACTCCGTCCCGATTCACCGGGGCTTAAACATCGGAAATCACCAACGTTCCTATTAT
+AACACCCAGCGTCAAGAGTTCGTAGGGTATGGTTATGGGAATTTAGCTGGAAGGTGTTACTACACGGGATCACCGTTGG
+ATCATAGGAACATTGTTGGATCAGAGCCGTTGGTTATAGACTCAGTCCCTGTGGTTCCCGGGAGATTAACTCCGGTGAT
+GTTACCGCCGCTTCCTCCGCCTCCTTCTACGGCGGGAAAGAGACTAAGGCTCTTTGGGGTGAATATGGAATGTGGCAAT
+GACTATAATCAACAAGAAGAGTCATGGTTGGTGCCACGTGGCGAAATTGGTGCATCTTCTTCTTCTTCTTCAGCTCTAC
+GACTAAATTTATCGACTGATCATGATGATGATAATGATGATGGTGATGATGGCGATGATGATCAATTTGCTAAGAAAGG
+GAAGTCTTCACTTTCTCTCAATTTCAATCCATGAGAAGTTTCATCATCTTCTTGTTTTGAATCTCTCTTTATATTGTTT
+CATTAGTAATTTTTCTAAGGGTATTAGATTCTAGCTAGTGAGAGGAAGAAAAAACGATCTTCTTCGTTTTTTTGGTTAT
+GATTTTTTTTTCCGACATGTTTCTTGATGTTCATCATCATTAGGCTTTTGTCACCATGTTGAAACTCGCATCTTTTCAA
+TTTTGTATATAA
+
+>arabidopsis2
+CTCCTCTGCCTCTCATCTCTTGTTCTCTCCGCCCATCTCTGCTCTCTTTTATTTTCCCAGAAAGTTTTTTTTTTTTTTT
+TCCGAATTCCGTTAATCTCATTGGGGTTTCCATTGATAGCAATGGCGACGGCTTTCGCTCCCACTAAGCTCACTGCCAC
+GGTTCCTCTGCATGGATCCCATGAGAATCGTCTCTTGCTCCCGATCCGATTGGCTCCTCCTTCTTCTTTCCTCGGATCC
+ACCCGTTCCCTCTCCCTTCGCAGACTCAATCACTCCAACGCCACCCGTCGATCTCCCGTCGTCTCTGTCCAGGAAGTTG
+TCAAGGAGAAGCAATCCACCAATAATACCAGCCTGGTACGCTTCCTCTCCTCGTCTCCTTCTTTTGGAATTTTACAAGT
+TGTGAGATTTGTTGTATTGATTTAAGTAATTTGAAATAGTTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATA
+TGATACTAGGTAGATCTTTCGAAGACATGTGTGCTCAAATGTATTACCGAGGCAAGATGTTTGGTTTTGTTCACTTGTA
+CAATGGCCAAGAGGCTGTTTCTACTGGCTTTATCAAGCTCCTTACCAAGTCTGACTCTGTCGTTAGTACCTACCGTGAC
+CATGTCCATGCCCTCAGCAAAGGTGTCTCTGCTCGTGCTGTTATGAGCGAGCTCTTCGGCAAGGTTACTGGATGCTGCA
+GAGGCCAAGGTGGATCCATGCACATGTTCTCCAAAGAACACAACATGCTTGGTGGCTTTGCTTTTATTGGTGAAGGCAT
+TCCTGTCGCCACTGGTGCTGCCTTTAGCTCCAAGTACAGGAGGGAAGTCTTGAAACAGGATTGTGATGATGTCACTGTC
+GCCTTTTTCGGAGATGGAACTTGTAACAACGGACAGTTCTTCGAGTGTCTCAACATGGCTGCTCTCTATAAACTGCCTA
+TTATCTTTGTTGTCGAGAATAACTTGTGGGCCATTGGGATGTCTCACTTGAGAGCCACTTCTGACCCCGAGATTTGGAA
+GAAAGGTCCTGCATTTGGGATGCCTGGTGTTCATGTTGACGGTATGGATGTCTTGAAGGTCAGGGAAGTCGCTAAAGAA
+GCTGTCACTAGAGCTAGAAGAGGAGAAGGTCCAACCTTGGTTGAATGTGAGACTTATAGATTCAGAGGACACTCCTTGG
+CTGATCCCGATGAGCTCCGTGATGCTGGTAAATATCGACTTCCTTCTGCTTCTTGATGCTTGTACTGATTATCTAAGGG
+TTGAAACAACCTTCTCTTTAATTTGAATTTTTTTTTGCAGCTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAG
+CATTGAAGAAGTATTTGATAGAGAACAAGCTTGCAAAGGAAGCAGAGCTAAAGTCAATAGAGAAAAAGATAGACGAGTT
+GGTGGAGGAAGCGGTTGAGTTTGCAGACGCTAGTCCACAGCCCGGTCGCAGTCAGTTGCTAGAGAATGTGTTTGCTGAT
+CCAAAAGGATTTGGAATTGGACCTGATGGACGGTACAGATGTGAGGACCCCAAGTTTACCGAAGGCACAGCTCAAGTCT
+GAGAAGACAAGTTTAACCATAAGCTGTCTACTGTCTCTTCGATGTTTCTATATATCTTATTAAGTTAAATGCTACAGAG
+AATCAGTTTGAATCATTTGCACTTTTTGCTTTTTGTTTGGTGTTACTAAACTATCACAAGGTTCTTCTTGTAGTTCGTT
+GGGTTTTCATTGGTTACCACTTACCAGAGAATTGTATTTTTTTTTTTAAAGATAATTATTTTGC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf	Sun Jun 09 07:54:25 2013 -0400
@@ -0,0 +1,85 @@
+# This output was generated with AUGUSTUS (version 2.7).
+# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.de)
+# and Oliver Keller (keller@cs.uni-goettingen.de).
+# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
+# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
+# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
+# No extrinsic information on sequences given.
+# arabidopsis version. Using default transition matrix.
+# We have hints for 0 sequences and for 0 of the sequences in the input set.
+#
+# ----- prediction on sequence number 1 (length = 2066, name = arabidopsis) -----
+#
+# Constraints/Hints:
+# (none)
+# Predicted genes for sequence number 1 on both strands
+# start gene g1
+arabidopsis	AUGUSTUS	gene	775	1851	0	+	.	g1
+arabidopsis	AUGUSTUS	transcript	775	1851	.	+	.	g1.t1
+arabidopsis	AUGUSTUS	start_codon	775	777	.	+	0	transcript_id "g1.t1"; gene_id "g1";
+arabidopsis	AUGUSTUS	CDS	775	1851	0.99	+	0	transcript_id "g1.t1"; gene_id "g1";
+arabidopsis	AUGUSTUS	stop_codon	1849	1851	.	+	0	transcript_id "g1.t1"; gene_id "g1";
+# protein sequence = [MDLSLAPTTTTSSDQEQDRDQELTSNIGASSSSGPSGNNNNLPMMMIPPPEKEHMFDKVVTPSDVGKLNRLVIPKQHA
+# ERYFPLDSSNNQNGTLLNFQDRNGKMWRFRYSYWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFQRGIGDESERSKLYIDWRHRPDMSLVQAHQFGNFG
+# FNFNFPTTSQYSNRFHPLPEYNSVPIHRGLNIGNHQRSYYNTQRQEFVGYGYGNLAGRCYYTGSPLDHRNIVGSEPLVIDSVPVVPGRLTPVMLPPLP
+# PPPSTAGKRLRLFGVNMECGNDYNQQEESWLVPRGEIGASSSSSSALRLNLSTDHDDDNDDGDDGDDDQFAKKGKSSLSLNFNP]
+# end gene g1
+###
+# start gene g2
+arabidopsis	AUGUSTUS	gene	841	1661	.	-	.	g2
+arabidopsis	AUGUSTUS	transcript	841	1661	.	-	.	g2.t1
+arabidopsis	AUGUSTUS	stop_codon	841	843	.	-	0	transcript_id "g2.t1"; gene_id "g2";
+arabidopsis	AUGUSTUS	intron	1024	1101	0.75	-	.	transcript_id "g2.t1"; gene_id "g2";
+arabidopsis	AUGUSTUS	intron	1193	1325	0.03	-	.	transcript_id "g2.t1"; gene_id "g2";
+arabidopsis	AUGUSTUS	intron	1416	1512	0.85	-	.	transcript_id "g2.t1"; gene_id "g2";
+arabidopsis	AUGUSTUS	CDS	841	1023	0.87	-	0	transcript_id "g2.t1"; gene_id "g2";
+arabidopsis	AUGUSTUS	CDS	1102	1192	0.78	-	1	transcript_id "g2.t1"; gene_id "g2";
+arabidopsis	AUGUSTUS	CDS	1326	1415	0.05	-	1	transcript_id "g2.t1"; gene_id "g2";
+arabidopsis	AUGUSTUS	CDS	1513	1661	0.35	-	0	transcript_id "g2.t1"; gene_id "g2";
+# protein sequence = [SLPHSIFTPKSLSLFPAVEGGGGSGGNITGVNLPGTTGTESITNGSDPTMNVGDFRCLSPGESGRSYILAMDEICWNI
+# EKDNVSCIELFLFDETAPSFGHNVALARVPIRREIPLSVLFRDHESVEFSDVAWCYHFVEHVFFLRRWNHHHRKVVVVSAGTGAAACSDVGG]
+# end gene g2
+###
+#
+# ----- prediction on sequence number 2 (length = 1802, name = arabidopsis2) -----
+#
+# Constraints/Hints:
+# (none)
+# Predicted genes for sequence number 2 on both strands
+# start gene g3
+arabidopsis2	AUGUSTUS	gene	97	1600	.	-	.	g3
+arabidopsis2	AUGUSTUS	transcript	97	1600	.	-	.	g3.t1
+arabidopsis2	AUGUSTUS	stop_codon	97	99	.	-	0	transcript_id "g3.t1"; gene_id "g3";
+arabidopsis2	AUGUSTUS	intron	349	521	0.73	-	.	transcript_id "g3.t1"; gene_id "g3";
+arabidopsis2	AUGUSTUS	intron	1210	1333	0.36	-	.	transcript_id "g3.t1"; gene_id "g3";
+arabidopsis2	AUGUSTUS	intron	1452	1560	0.54	-	.	transcript_id "g3.t1"; gene_id "g3";
+arabidopsis2	AUGUSTUS	CDS	97	348	0.73	-	0	transcript_id "g3.t1"; gene_id "g3";
+arabidopsis2	AUGUSTUS	CDS	522	1209	0.6	-	1	transcript_id "g3.t1"; gene_id "g3";
+arabidopsis2	AUGUSTUS	CDS	1334	1451	0.44	-	2	transcript_id "g3.t1"; gene_id "g3";
+arabidopsis2	AUGUSTUS	CDS	1561	1600	0.42	-	0	transcript_id "g3.t1"; gene_id "g3";
+arabidopsis2	AUGUSTUS	start_codon	1598	1600	.	-	0	transcript_id "g3.t1"; gene_id "g3";
+# protein sequence = [MVKLVFSDLSCAFASANSTASSTNSSIFFSIDFSSASFASLFSIKYFFNAAIGITELIGISQGVSSESISLTFNQGWT
+# FSSSSSSDSFFSDFPDLQDIHTVNMNTRHPKCRTFLPNLGVRSGSQVRHPNGPQVILDNKDNRQFIESSHVETLEELSVVTSSISEKGDSDIITILFQ
+# DFPPVLGAKGSTSGDRNAFTNKSKATKHVVFFGEHVHGSTLASAASSNLAEELAHNSTSRDTFAEGMDMVTVGTNDRVRLGKELDKASRNSLLAIVQV
+# NKTKHLASAGIIGGLLLLDNFLDRDDGRSTGGVGVIESAKGEGTGGSEERRRRSQSDREQETILMGSMQRNRGSELSGSESRRHCYQWKPQ]
+# end gene g3
+###
+# start gene g4
+arabidopsis2	AUGUSTUS	gene	121	1582	0	+	.	g4
+arabidopsis2	AUGUSTUS	transcript	121	1582	.	+	.	g4.t1
+arabidopsis2	AUGUSTUS	start_codon	121	123	.	+	0	transcript_id "g4.t1"; gene_id "g4";
+arabidopsis2	AUGUSTUS	intron	352	434	0.97	+	.	transcript_id "g4.t1"; gene_id "g4";
+arabidopsis2	AUGUSTUS	intron	1213	1304	1	+	.	transcript_id "g4.t1"; gene_id "g4";
+arabidopsis2	AUGUSTUS	CDS	121	351	0.72	+	0	transcript_id "g4.t1"; gene_id "g4";
+arabidopsis2	AUGUSTUS	CDS	435	1212	0.97	+	0	transcript_id "g4.t1"; gene_id "g4";
+arabidopsis2	AUGUSTUS	CDS	1305	1582	1	+	2	transcript_id "g4.t1"; gene_id "g4";
+arabidopsis2	AUGUSTUS	stop_codon	1580	1582	.	+	0	transcript_id "g4.t1"; gene_id "g4";
+# protein sequence = [MATAFAPTKLTATVPLHGSHENRLLLPIRLAPPSSFLGSTRSLSLRRLNHSNATRRSPVVSVQEVVKEKQSTNNTSLL
+# ITKEEGLELYEDMILGRSFEDMCAQMYYRGKMFGFVHLYNGQEAVSTGFIKLLTKSDSVVSTYRDHVHALSKGVSARAVMSELFGKVTGCCRGQGGSM
+# HMFSKEHNMLGGFAFIGEGIPVATGAAFSSKYRREVLKQDCDDVTVAFFGDGTCNNGQFFECLNMAALYKLPIIFVVENNLWAIGMSHLRATSDPEIW
+# KKGPAFGMPGVHVDGMDVLKVREVAKEAVTRARRGEGPTLVECETYRFRGHSLADPDELRDAAEKAKYAARDPIAALKKYLIENKLAKEAELKSIEKK
+# IDELVEEAVEFADASPQPGRSQLLENVFADPKGFGIGPDGRYRCEDPKFTEGTAQV]
+# end gene g4
+###
+# command line:
+# ./bin/augustus --species=arabidopsis --UTR=off --singlestrand=true --mea=1 /home/bag/projects/github/galaxytools/augustus/test-data/arabidopsis_augustus.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus.fa	Sun Jun 09 07:54:25 2013 -0400
@@ -0,0 +1,200 @@
+>HS04636
+gagctcacattaactatttacagggtaactgcttaggaccagtattatgaggagaattta
+cctttcccgcctctctttccaagaaacaaggagggggtgaaggtacggagaacagtattt
+cttctgttgaaagcaacttagctacaaagataaattacagctatgtacactgaaggtagc
+tatttcattccacaaaataagagttttttaaaaagctatgtatgtatgtgctgcatatag
+agcagatatacagcctattaagcgtcgtcactaaaacataaaacatgtcagcctttctta
+accttactcgccccagtctgtcccgacgtgacttcctcgaccctctaaagacgtacagac
+cagacacggcggcggcggcgggagaggggattccctgcgcccccggacctcagggccgct
+cagattcctggagaggaagccaagtgtccttctgccctcccccggtatcccatccaaggc
+gatcagtccagaactggctctcggaagcgctcgggcaaagactgcgaagaagaaaagaca
+tctggcggaaacctgtgcgcctggggcggtggaactcggggaggagagggagggatcaga
+caggagagtggggactaccccctctgctcccaaattggggcagcttcctgggtttccgat
+tttctcatttccgtgggtaaaaaaccctgcccccaccgggcttacgcaatttttttaagg
+ggagaggagggaaaaaatttgtgggggggtacgaaaaggcggaaagaaacagtcattcac
+atgggcttggttttcagtcttataaaaaggaaggttctctcggttagcgaccaattgtca
+tacgacttgcagtgagcgtcaggagcacgtccaggaactcctcagcagcgcctccttcag
+ctccacagccagacgccctcagacagcaaagcctacccccgcgccgcgccctgcccgccg
+ctcggatgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacaggtg
+agtacctggcgccgcgcaccggggactccggttccacgcacccgggcagagtttccgctc
+tgacctcctgggtctatcccagtactccgacttctctccgaatagagaagctacgtgact
+tgggaaagagcttggaccgctagagtccgaaagaactccgtggatattccagctttccca
+caagcactgatcattatgagccagttacttaaccgatctgagacactctcacctcctaaa
+tagggatagatgatactaatttgcaggttgtcattatgataagacaggatctgatcaata
+tatgtgaattgtttatatttggaacctttttattgagtggaagaagttgttttaaatatt
+ctagtcagttctttcctgctcccaggaaagcccggattatgttttaagataagcaaaatg
+tcttaaaagtaagctgttttactttgaatttttccctaaatgttgattagtgtactagat
+ccattttaatttggaaagtgaagtgctacttatttgaacttcttaaaaatgctaatttta
+acatctaaagagttaactaagaaaagcttagtaacatgatgtaccaagttgaatatgctg
+ttatccttatttagaatagaaaattggtatttctacgttttatccattctaaggcaggtt
+aaaaaattgtatttccatgactacctatatatttcttgaatttattattgtaaagttgat
+tcatagtcaaacaattaaatgtttaaattaagattaagacactagagaatgatttatttg
+ctgtcctttaattgcagcaaatccttgctgttcccacccatgtcaaaaccgaggtgtatg
+tatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggaga
+aaactgctcaacacgtaagtttgtcctttggttgcctcattaggagtggggctggataca
+gttatcattgtatagatttgtgtcttataatgagtcccattaatttctccctccctttct
+tcgtcttcttgcagcggaatttttgacaagaataaaattatttctgaaacccactccaaa
+cacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc
+cttccttcgaaatgcaattatgagttatgtcttgacatgtaagtacaagtgtctttctaa
+ggtttttagccttctcaaagaaaaatatgctttataatactgtaagcctaatctaaaaac
+atatttccaagcttatcaaaaagactttaagatagcttttaagtttgccttccatcttaa
+tcgccaaaaatattgacatttagtcccatccagtttatacagtctgctcacaactctgta
+tacctcttctaacctttactgtttggtcagtttgtggaggtagcatggtccagctgttta
+ttgaatgcccatgggccacagaattgttctgaacatgtagcacccattaaaataaatttg
+gatttggatcagcaagaaaataactttccatgattctaaagtgggtgccatactcagcca
+ttcctttcataggcctcttggatagtgagcagatggctacctgaaaaatcaatattgcca
+gattataatgtgcagagtatatgtattttattaaagatgtatttcaagtggccattagac
+tataaagtgtagttgtttaaaaatagattttttttattttggagttacattcaacctcag
+gtgccactttccacattttacaataaaaataatggttgatttacttaacaaatgagaata
+aataaaacatttttttctttgaaaatttcagccagatcacatttgattgacagtccacca
+acttacaatgctgactatggctacaaaagctgggaagccttctctaacctctcctattat
+actagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtgag
+taagaagaatccattagagatgtattaactataagacgggctgcattgctgccaaaaaaa
+aaaattgaccttagactaccatttatttattaacaaaagcagtttttacttttagcatgg
+ttatctatgggtattttttaaagtatgagtctatataaactattatgtaaaagcaaatga
+gcgtcttggtataatgtcttaatattttcaaattatttctttagaaatgaaataattcta
+attaaaatagataaaatcattcagtaagaagttgttccaccatatcttagaactgttgtt
+tatattatgatcctattcacaattgtaattctcatataaatgaagaattcttggtagatt
+gacagtcaccatctcctttcttgaatacatagatggattcttaccttagctttctcattt
+ttcaggtaaaaagcagcttcctgattcaaatgagattgtggaaaaattgcttctaagaag
+aaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagcactt
+cacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctggg
+ccatggggtaagatagagttaatatcttagagttagtaaaattataccaaatcatagtca
+agggctaacattaaaggagatatacagatagatagatccaaataacttatccactttttt
+taaaaagaagtcttatctataaaaaccttaaaggaattttccatttacttcactggtcta
+gtaaaattatacacacacacagacatgcacacacatatataaacattcacacacatacat
+atgtacaggtattgttatttgtaatttgacccttgtattttttagtttaaaatgttagta
+ctgcaaaatgttatgtcctcaaaaacacattgtaccatgattatgccgctttcaatattg
+taaagtgaggtttttgccgcattattattttttggatttcaatagcatagcttcaagtta
+ttcgtaagaattttttataaataatacatttttatacttttttataattaccatatcatc
+atagtgaagtatataatatatatgatataagctcaatatagtatattaattccgttaaac
+acaaagacatatcagtttgtagctttggtggataaacaaattaatttagcaattcatggc
+tatgaaaaatgtatattttatttaaaaattttaaagaaagctaaatgatcaaattattta
+atgatgaattatatgatagacactttatataagaaaaacttcaacagcaacaaattaaaa
+ttttttcatcattttctaggtggacttaaatcatatttacggtgaaactctggctagaca
+gcgtaaactgcgccttttcaaggatggaaaaatgaaatatcaggtatgcttcctttgact
+attaagacttagttattaccgcttatacccatattttaaaatccctaaaaatgtgttcct
+taactttttaactgatgtttatttatttatttatttttttagataattgatggagagatg
+tatcctcccacagtcaaagatactcaggcagagatgatctaccctcctcaagtccctgag
+catctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtat
+gccacaatctggctgcgggaacacaacagagtatgcgatgtgcttaaacaggagcatcct
+gaatggggtgatgagcagttgttccagacaagcaggctaatactgataggtaaacaagaa
+aatgatttatataaaaccctcttccccagggaaaattagtgtgctatctttgttatgttt
+tgagtaaatgacaagatgtggtaaatgaaaactcacacattctatatacattaaatatgt
+aagcatgactgataaaatagctatcttttgatactgacaaggaagaaaacagaaatgaag
+gaatagcaaattttaaaaattgcattccagttgcttgaaagcttgtgatcagatgcaata
+aatgtttttattatttattttgtgcaaataggagagactattaagattgtgattgaagat
+tatgtgcaacacttgagtggctatcacttcaaactgaaatttgacccagaactacttttc
+aacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactgg
+catccccttctgcctgacacctttcaaattcatgaccagaaatacaactatcaacagttt
+atctacaacaactctatattgctggaacatggaattacccagtttgttgaatcattcacc
+aggcaaattgctggcagggtaagcattattattgaaaaccaaaacaaaagactagtcagt
+aactttagaatttctgccacggaaattatttttcttaaacttactaaaagagtagttagt
+tatattgctagtaaaattattttattgatataagaagcctaactttgtttgaaaagtcta
+aacttttagtctagtctacagttgtcagacaaatagcaaattgtacccctaccttaaaaa
+tattttcaaaaagtatctataatcttataggaataaatattttaggcttgaatactagtg
+ttatttttgaaatgtaaaaaggcaaattagttctaggctggtgtcccattgaattttaag
+cagagctcctgttgaaatgtaggtaagcatctttccagcaaataaaaattgtctccgctg
+ggagtttcagttttacctgatttgtacctaaggcaagctgaatacaaacagtaaatatgc
+ctaaaattcttgttttacaactaattttactttccacaggttgctggtggtaggaatgtt
+ccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaatac
+cagtcttttaatgagtaccgcaaacgctttatgctgaagccctatgaatcatttgaagaa
+cttacaggtaagaaacagtttctaaacttcttcgttttttgtttgtttgtttgtttttgt
+tgtttttggttttcttttcgagatggagccgccctctgtcacccaggctggagtgcagtg
+gcgccatctcggctcactgcaacctccgcctcctgggttcaagcaattctcctgcctcaa
+cttcctgagtagctgggactacaggctcacgtcgcacgcatggataattttttgtatttt
+cagtatagacggggtttcaccgtgttagccaggctggtctcaaactcctgacctagtgat
+ccgccggcttcggcctcccgaagtgctgggattacaggcgtgagccaccgcgcctggccc
+ctaaacttcttaaaagaatcaggggtcaaatggaaacagagaagttggcagcaaattgag
+caaaagaatcaaactgttttttattttgtgaagtttgacattggttgtatctctgtcttc
+atcgccttcacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacatc
+gatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatcttt
+ggtgaaaccatggtagaagttggagcaccattctccttgaaaggacttatgggtaatgtt
+atatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatc
+atcaacactgcctcaattcagtctctcatctgcaataacgtgaagggctgtccctttact
+tcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaagttcttcc
+cgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactg
+tagaagtctaatgatcatatttatttatttatatgaaccatgtctattaatttaattatt
+taataatatttatattaaactccttatgttacttaacatcttctgtaacagaagtcagta
+ctcctgttgcggagaaaggagtcatacttgtgaagacttttatgtcactactctaaagat
+tttgctgttgctgttaagtttggaaaacagtttttattctgttttataaaccagagagaa
+atgagttttgacgtctttttacttgaatttcaacttatattataagaacgaaagtaaaga
+tgtttgaatacttaaacactatcacaagatggcaaaatgctgaaagtttttacactgtcg
+atgtttccaatgcatcttccatgatgcattagaagtaactaatgtttgaaattttaaagt
+acttttggttatttttctgtcatcaaacaaaaacaggtatcagtgcattattaaatgaat
+atttaaattagacattaccagtaatttcatgtctactttttaaaatcagcaatgaaacaa
+taatttgaaatttctaaattcatagggtagaatcacctgtaaaagcttgtttgatttctt
+aaagttattaaacttgtacatataccaaaaagaagctgtcttggatttaaatctgtaaaa
+tcagatgaaattttactacaattgcttgttaaaatattttataagtgatgttcctttttc
+accaagagtataaacctttttagtgtgactgttaaaacttccttttaaatcaaaatgcca
+aatttattaaggtggtggagccactgcagtgttatctcaaaataagaatattttgttgag
+atattccagaatttgtttatatggctggtaacatgtaaaatctatatcagcaaaagggtc
+tacctttaaaataagcaataacaaagaagaaaaccaaattattgttcaaatttaggttta
+aacttttgaagcaaacttttttttatccttgtgcactgcaggcctggtactcagattttg
+ctatgaggttaatgaagtaccaagctgtgcttgaataacgatatgttttctcagattttc
+tgttgtacagtttaatttagcagtccatatcacattgcaaaagtagcaatgacctcataa
+aatacctcttcaaaatgcttaaattcatttcacacattaattttatctcagtcttgaagc
+caattcagtaggtgcattggaatcaagcctggctacctgcatgctgttccttttcttttc
+ttcttttagccattttgctaagagacacagtcttctcatcacttcgtttctcctattttg
+ttttactagttttaagatcagagttcactttctttggactctgcctatattttcttacct
+gaacttttgcaagttttcaggtaaacctcagctcaggactgctatttagctcctcttaag
+aagattaaaagagaaaaaaaaaggcccttttaaaaatagtatacacttattttaagtgaa
+aagcagagaattttatttatagctaattttagctatctgtaaccaagatggatgcaaaga
+ggctagtgcctcagagagaactgtacggggtttgtgactggaaaaagttacgttcccatt
+ctaattaatgccctttcttatttaaaaacaaaaccaaatgatatctaagtagttctcagc
+aataataataatgacgataatacttcttttccacatctcattgtcactgacatttaatgg
+tactgtatattacttaatttattgaagattattatttatgtcttattaggacactatggt
+tataaactgtgtttaagcctacaatcattgatttttttttgttatgtcacaatcagtata
+ttttctttggggttacctctctgaatattatgtaaacaatccaaagaaatgattgtatta
+agatttgtgaataaatttttagaaatctgattggcatattgagatatttaaggttgaatg
+tttgtccttaggataggcctatgtgctagcccacaaagaatattgtctcattagcctgaa
+tgtgccataagactgaccttttaaaatgttttgagggatctgtggatgcttcgttaattt
+gttcagccacaatttattgagaaaatattctgtgtcaagcactgtgggttttaatatttt
+taaatcaaacgctgattacagataatagtatttatataaataattgaaaaaaattttctt
+ttgggaagagggagaaaatgaaataaatatcattaaagataactcaggagaatcttcttt
+acaattttacgtttagaatgtttaaggttaagaaagaaatagtcaatatgcttgtataaa
+acactgttcactgttttttttaaaaaaaaaacttgatttgttattaacattgatctgctg
+acaaaacctgggaatttgggttgtgtatgcgaatgtttcagtgcctcagacaaatgtgta
+tttaacttatgtaaaagataagtctggaaataaatgtctgtttatttttgtactatttaa
+aaaaaaaaaaaaaaatcgatgtcgactcgagtc
+>HS08198
+agcgggcggcggtcgtgggcggggttgcaggcgaggctcaacgaacgctggtctgaccgt
+cggcgctccctgttgccgggccctgagcaagtggcttcatgaaccccgtgacgttggcca
+tggagataagaccactgggtgatggtttaaggaagataacgtgtaaagggctaaggactg
+tcggtggaaatcaggggtgcaggagaaatggataaacagccagaggtcaactcggacttt
+gtacataggacatggtgccaggccctgccaggaagtgcagatcgaagctaggctcacgag
+gaggctggaggtggggggtggggaggcaacggatggacatggacttcctgggctgggctc
+tgtgacagcagagtagactctgtcctgggacttggtggtgctacccttggcctcccacag
+tcctgccaccctgctgccgccaccatgctgccccctgggactgcgaccctcttgactctg
+ctcctggcagctggctcgctgggccagaagcctcagaggccacgccggcccgcatccccc
+atcagcaccatccagcccaaggccaattttgatgcgcagcaggtagaagttggggggggt
+agagggaggcaggtagaagttgtgggaggggtagagggagacaggtagaagttgttgcgg
+gggagagggaagcaggtgaagttgtggggggtgtagagggaagcaggtgaggggccctcc
+cacagtgccctcgagttctcccatggtctgcccccagtttgcagggacctggctccttgt
+ggctgtgggctccgcttgccgtttcctgcaggagcagggccaccgggccgaggccaccac
+actgcatgtggctccccagggcacagccatggctgtcagtaccttccgaaagctgtgagt
+cccagagcagccctgcaccctaaccccaaccctcctctcagcccccggacttcagccctg
+ctctggcccctgaccccaccccggctgtggcctggactaggattcctggttggggtctcc
+cagcctgtggtgcctcctccccgcccccccagggatgggatctgctggcaggtgcgccag
+ctctatggagacacaggggtcctcggccgcttcctgcttcaaggtgaggcaggggctgca
+ggtcatgtgggtgggggatgacgcagccactgtggctctctgacatggctactgtggctc
+tgcccagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccag
+agtttcgctgtcctgtacctggagcgggcggggcagctgtcagtgaagctctacggtatg
+tgggggccagcctctgtgaccaggcaggcgctcaagctctgcacactcactgggccaccc
+cgaggggctgggtgagccatggggacacacttcctttctcccatcctgatcctcctgcta
+agcaggggcccagggagtagtgacagacaggcctggtgtgggagcagggaggagggcccc
+gaggggcaggggacacacagaccccgttcccagagccctccacgccgcctggtgccagga
+ccccaggaaccctgtctgccctgcagcccgctcgctccctgtgagcgactcggtcctgag
+tgggtttgagcagcgggtccaggaggcccacctgactgaggaccagatcttctacttccc
+caagtacggtgagtgtccccagcaggtccccagctcagccacccccactctctggctgat
+gtccagcctgacccctgccttggcgccccaggcttctgcgaggctgcagaccagttccac
+gtcctggacggtgagtgcacagcgggggcaagcatggcggcgtggtgaggggggccactc
+gcaccggctgagtctcgtctctgctgcagaagtgaggaggtgaggccggcacacagctcc
+agtgctgagaagtcagtgccccgagagacgaccccaccagtggggtgcccgctgcctgtc
+ctccgtgaaaccagcctcagatcagggccctgccacccagggcaggggatcttctgccgg
+ctgccccagaggacagtgggtggagtggtacctacttattaaatgtctcagacccctctc
+tgactcttctgtccactctggaccggcgccagtaccaccaaggccctctctgcccccacc
+ccgcctctttaaaagcccggcgctccctgttggctggagtccacgcagggtcactgggcc
+gatttcggctcttgggatttgggaggggagatcctctctggcatatgccatcttgtgccc
+tgctggacctgggggcgtccacgtcactccaaggctgctcttgcctgggccatgcctgca
+gccc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus_protein_codingseq_introns_cds_codingseq.fasta	Sun Jun 09 07:54:25 2013 -0400
@@ -0,0 +1,35 @@
+>g1
+atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtca
+tgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtcaa
+aaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactg
+ctcaacaccggaatttttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccact
+tcaagggattttggaacgttgtgaataacattcccttccttcgaaatgcaattatgagttatgtcttgacatccagatca
+catttgattgacagtccaccaacttacaatgctgactatggctacaaaagctgggaagccttctctaacctctcctatta
+tactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagcttcctgattcaa
+atgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattcttt
+gcccagcacttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggt
+ggacttaaatcatatttacggtgaaactctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatc
+agataattgatggagagatgtatcctcccacagtcaaagatactcaggcagagatgatctaccctcctcaagtccctgag
+catctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgccacaatctggctgcggga
+acacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa
+tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaattt
+gacccagaactacttttcaacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggca
+tccccttctgcctgacacctttcaaattcatgaccagaaatacaactatcaacagtttatctacaacaactctatattgc
+tggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggcagggttgctggtggtaggaatgttcca
+cccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgagtaccgcaa
+acgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactct
+atggtgacatcgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaacc
+atggtagaagttggagcaccattctccttgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaag
+cacttttggtggagaagtgggttttcaaatcatcaacactgcctcaattcagtctctcatctgcaataacgtgaagggct
+gtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaagttcttcccgctccgga
+ctagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag
+>g2
+atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccaca
+tgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccacgc
+cggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggc
+caccacactgcatgtggctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcagg
+tgcgccagctctatggagacacaggggtcctcggccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtg
+gttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcgggcggggcagctgtcagtgaagctctacgc
+ccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgactgaggaccaga
+tcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggca
+agcatggcggcgtggtga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf	Sun Jun 09 07:54:25 2013 -0400
@@ -0,0 +1,101 @@
+# This output was generated with AUGUSTUS (version 2.7).
+# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.de)
+# and Oliver Keller (keller@cs.uni-goettingen.de).
+# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
+# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
+# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
+# No extrinsic information on sequences given.
+# Initialising the parameters ...
+# human version. Using default transition matrix.
+# Looks like /home/bag/projects/galaxy/galaxy-central/database/files/001/dataset_1149.dat is in fasta format.
+# We have hints for 0 sequences and for 0 of the sequences in the input set.
+#
+# ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
+#
+# Constraints/Hints:
+# (none)
+# Predicted genes for sequence number 1 on both strands
+# start gene g1
+HS04636	AUGUSTUS	gene	966	6903	1	+	.	g1
+HS04636	AUGUSTUS	transcript	966	6903	.	+	.	g1.t1
+HS04636	AUGUSTUS	intron	1018	1817	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	intron	1935	2054	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	intron	2199	2851	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	intron	2996	3425	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	intron	3608	4339	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	intron	4424	4542	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	intron	4790	5071	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	intron	5359	5859	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	intron	6008	6493	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	966	1017	.	+	0	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	1818	1934	.	+	2	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	2055	2198	.	+	2	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	2852	2995	.	+	2	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	3426	3607	.	+	2	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	4340	4423	.	+	0	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	4543	4789	.	+	0	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	5072	5358	.	+	2	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	5860	6007	.	+	0	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	6494	6903	.	+	2	transcript_id "g1.t1"; gene_id "g1";
+# coding sequence = [atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtc
+# aaaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccggaattt
+# ttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc
+# cttccttcgaaatgcaattatgagttatgtcttgacatccagatcacatttgattgacagtccaccaacttacaatgctgactatggctacaaaagct
+# gggaagccttctctaacctctcctattatactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagctt
+# cctgattcaaatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagca
+# cttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggtggacttaaatcatatttacggtgaaa
+# ctctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatcagataattgatggagagatgtatcctcccacagtcaaagatact
+# caggcagagatgatctaccctcctcaagtccctgagcatctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgc
+# cacaatctggctgcgggaacacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa
+# tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaatttgacccagaactacttttc
+# aacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggcatccccttctgcctgacacctttcaaattcatgacca
+# gaaatacaactatcaacagtttatctacaacaactctatattgctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggca
+# gggttgctggtggtaggaatgttccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgag
+# taccgcaaacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacat
+# cgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaaccatggtagaagttggagcaccattctcct
+# tgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatcatcaacactgcctca
+# attcagtctctcatctgcaataacgtgaagggctgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaag
+# ttcttcccgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag]
+# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
+# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
+# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
+# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
+# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
+# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
+# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
+# end gene g1
+###
+#
+# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
+#
+# Constraints/Hints:
+# (none)
+# Predicted genes for sequence number 2 on both strands
+# start gene g2
+HS08198	AUGUSTUS	gene	445	1848	1	+	.	g2
+HS08198	AUGUSTUS	transcript	445	1848	.	+	.	g2.t1
+HS08198	AUGUSTUS	intron	583	811	.	+	.	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	intron	895	1052	.	+	.	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	intron	1124	1207	.	+	.	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	intron	1316	1586	.	+	.	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	intron	1689	1771	.	+	.	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	CDS	445	582	.	+	0	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	CDS	812	894	.	+	0	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	CDS	1053	1123	.	+	1	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	CDS	1208	1315	.	+	2	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	CDS	1587	1688	.	+	2	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	CDS	1772	1848	.	+	2	transcript_id "g2.t1"; gene_id "g2";
+# coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac
+# gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg
+# gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg
+# ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg
+# cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact
+# gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc
+# ggcgtggtga]
+# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
+# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
+# HVLDGECTAGASMAAW]
+# end gene g2
+###
+# command line:
+# augustus --strand=both --noInFrameStop=false --gff3=off --protein=on --introns=on --start=off --stop=off --cds=on --codingseq=on --singlestrand=false /home/bag/projects/galaxy/galaxy-central/database/files/001/dataset_1149.dat --UTR=off --genemodel=complete --species=human
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus_protein_codingseq_introns_cds_protein.fasta	Sun Jun 09 07:54:25 2013 -0400
@@ -0,0 +1,15 @@
+>g1
+MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILML
+ARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTHFK
+GFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNE
+IVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQI
+IDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLIL
+IGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSILLE
+HGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYG
+DIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCP
+FTSFSVPDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL
+>g2
+MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICML
+PPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICWQVR
+QLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIF
+YFPKYGFCEAADQFHVLDGECTAGASMAAW
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus_utr-on.gff	Sun Jun 09 07:54:25 2013 -0400
@@ -0,0 +1,77 @@
+##gff-version 3
+# This output was generated with AUGUSTUS (version 2.7).
+# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.de)
+# and Oliver Keller (keller@cs.uni-goettingen.de).
+# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
+# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
+# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
+# No extrinsic information on sequences given.
+# Initialising the parameters ...
+# human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl
+# Looks like ./examples/example.fa is in fasta format.
+# We have hints for 0 sequences and for 0 of the sequences in the input set.
+#
+# ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
+#
+# Predicted genes for sequence number 1 on both strands
+# start gene g1
+HS04636	AUGUSTUS	gene	836	8857	1	+	.	ID=g1
+HS04636	AUGUSTUS	transcript	836	8857	.	+	.	ID=g1.t1;Parent=g1
+HS04636	AUGUSTUS	transcription_start_site	836	836	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	exon	836	1017	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	start_codon	966	968	.	+	0	Parent=g1.t1
+HS04636	AUGUSTUS	CDS	966	1017	.	+	0	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	CDS	1818	1934	.	+	2	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	exon	1818	1934	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	CDS	2055	2198	.	+	2	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	exon	2055	2198	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	CDS	2852	2995	.	+	2	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	exon	2852	2995	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	CDS	3426	3607	.	+	2	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	exon	3426	3607	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	CDS	4340	4423	.	+	0	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	exon	4340	4423	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	CDS	4543	4789	.	+	0	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	exon	4543	4789	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	CDS	5072	5358	.	+	2	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	exon	5072	5358	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	CDS	5860	6007	.	+	0	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	exon	5860	6007	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	CDS	6494	6903	.	+	2	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	exon	6494	8857	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	stop_codon	6901	6903	.	+	0	Parent=g1.t1
+HS04636	AUGUSTUS	transcription_end_site	8857	8857	.	+	.	Parent=g1.t1
+# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
+# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
+# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
+# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
+# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
+# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
+# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
+# end gene g1
+###
+#
+# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
+#
+# Predicted genes for sequence number 2 on both strands
+# start gene g2
+HS08198	AUGUSTUS	gene	86	2344	1	+	.	ID=g2
+HS08198	AUGUSTUS	transcript	86	2344	.	+	.	ID=g2.t1;Parent=g2
+HS08198	AUGUSTUS	transcription_start_site	86	86	.	+	.	Parent=g2.t1
+HS08198	AUGUSTUS	exon	86	582	.	+	.	Parent=g2.t1
+HS08198	AUGUSTUS	start_codon	445	447	.	+	0	Parent=g2.t1
+HS08198	AUGUSTUS	CDS	445	582	.	+	0	ID=g2.t1.cds;Parent=g2.t1
+HS08198	AUGUSTUS	CDS	812	894	.	+	0	ID=g2.t1.cds;Parent=g2.t1
+HS08198	AUGUSTUS	exon	812	894	.	+	.	Parent=g2.t1
+HS08198	AUGUSTUS	CDS	1053	1123	.	+	1	ID=g2.t1.cds;Parent=g2.t1
+HS08198	AUGUSTUS	exon	1053	1123	.	+	.	Parent=g2.t1
+HS08198	AUGUSTUS	CDS	1208	1315	.	+	2	ID=g2.t1.cds;Parent=g2.t1
+HS08198	AUGUSTUS	exon	1208	1315	.	+	.	Parent=g2.t1
+HS08198	AUGUSTUS	CDS	1587	1688	.	+	2	ID=g2.t1.cds;Parent=g2.t1
+HS08198	AUGUSTUS	exon	1587	1688	.	+	.	Parent=g2.t1
+# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
+# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY]
+# end gene g2
+###
+# command line:
+# ./bin/augustus --species=human --UTR=on --gff3=on ./examples/example.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus_utr-on.gtf	Sun Jun 09 07:54:25 2013 -0400
@@ -0,0 +1,80 @@
+# This output was generated with AUGUSTUS (version 2.7).
+# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.de)
+# and Oliver Keller (keller@cs.uni-goettingen.de).
+# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
+# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
+# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
+# No extrinsic information on sequences given.
+# Initialising the parameters ...
+# human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl
+# Looks like ./examples/example.fa is in fasta format.
+# We have hints for 0 sequences and for 0 of the sequences in the input set.
+#
+# ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
+#
+# Constraints/Hints:
+# (none)
+# Predicted genes for sequence number 1 on both strands
+# start gene g1
+HS04636	AUGUSTUS	gene	836	8857	1	+	.	g1
+HS04636	AUGUSTUS	transcript	836	8857	.	+	.	g1.t1
+HS04636	AUGUSTUS	tss	836	836	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	exon	836	1017	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	start_codon	966	968	.	+	0	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	966	1017	.	+	0	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	1818	1934	.	+	2	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	exon	1818	1934	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	2055	2198	.	+	2	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	exon	2055	2198	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	2852	2995	.	+	2	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	exon	2852	2995	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	3426	3607	.	+	2	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	exon	3426	3607	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	4340	4423	.	+	0	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	exon	4340	4423	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	4543	4789	.	+	0	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	exon	4543	4789	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	5072	5358	.	+	2	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	exon	5072	5358	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	5860	6007	.	+	0	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	exon	5860	6007	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	CDS	6494	6903	.	+	2	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	exon	6494	8857	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	stop_codon	6901	6903	.	+	0	transcript_id "g1.t1"; gene_id "g1";
+HS04636	AUGUSTUS	tts	8857	8857	.	+	.	transcript_id "g1.t1"; gene_id "g1";
+# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
+# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
+# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
+# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
+# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
+# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
+# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
+# end gene g1
+###
+#
+# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
+#
+# Constraints/Hints:
+# (none)
+# Predicted genes for sequence number 2 on both strands
+# start gene g2
+HS08198	AUGUSTUS	gene	86	2344	1	+	.	g2
+HS08198	AUGUSTUS	transcript	86	2344	.	+	.	g2.t1
+HS08198	AUGUSTUS	tss	86	86	.	+	.	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	exon	86	582	.	+	.	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	start_codon	445	447	.	+	0	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	CDS	445	582	.	+	0	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	CDS	812	894	.	+	0	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	exon	812	894	.	+	.	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	CDS	1053	1123	.	+	1	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	exon	1053	1123	.	+	.	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	CDS	1208	1315	.	+	2	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	exon	1208	1315	.	+	.	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	CDS	1587	1688	.	+	2	transcript_id "g2.t1"; gene_id "g2";
+HS08198	AUGUSTUS	exon	1587	1688	.	+	.	transcript_id "g2.t1"; gene_id "g2";
+# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
+# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY]
+# end gene g2
+###
+# command line:
+# ./bin/augustus --species=human --UTR=on ./examples/example.fa
--- a/tool_dependencies.xml	Tue Oct 30 06:29:50 2012 -0400
+++ b/tool_dependencies.xml	Sun Jun 09 07:54:25 2013 -0400
@@ -1,10 +1,12 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="augustus" version="2.6.1">
+    <set_environment version="1.0">
+        <environment_variable name="AUGUSTUS_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+    <package name="augustus" version="2.7">
         <install version="1.0">
             <actions>
-                <!-- the first command puts us in the dir for the package name: "augustus"-->
-                <action type="download_by_url">http://bioinf.uni-greifswald.de/augustus/binaries/augustus.2.6.1.tar.gz</action>
+                <action type="download_by_url">http://bioinf.uni-greifswald.de/augustus/binaries/augustus.2.7.tar.gz</action>
                 <action type="shell_command">make</action>
                 <action type="move_directory_files">
                     <source_directory>bin</source_directory>
@@ -20,15 +22,15 @@
                 </action>
                 <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
-                </action>
-                <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-                <action type="set_environment">
                     <environment_variable name="AUGUSTUS_CONFIG_PATH" action="set_to">$INSTALL_DIR/config</environment_variable>
                 </action>
             </actions>
         </install>
-        <readme>http://augustus.gobics.de/binaries/README.TXT</readme>
+        <readme>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.
+http://augustus.gobics.de/binaries/README.TXT</readme>
     </package>
 </tool_dependency>