# HG changeset patch
# User iuc
# Date 1432284925 14400
# Node ID f5075dee9d6b4e250f0894579082c341173bbf4f
# Parent  a77a4e9921e0e0c20b94686348d56c3f1ca49b0b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac

diff -r a77a4e9921e0 -r f5075dee9d6b augustus.xml
--- a/augustus.xml	Wed May 06 14:31:02 2015 -0400
+++ b/augustus.xml	Fri May 22 04:55:25 2015 -0400
@@ -1,8 +1,8 @@
-<tool id="augustus" name="Augustus" version="0.3.1">
+<tool id="augustus" name="Augustus" version="3.1.0">
     <description>gene prediction for eukaryotic genomes</description>
     <parallelism method="multi" split_inputs="input_genome" split_mode="to_size" split_size="10" merge_outputs="output,protein_output,codingseq_output"></parallelism>
     <requirements>
-        <requirement type="package" version="2.7">augustus</requirement>
+        <requirement type="package" version="3.1">augustus</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -12,14 +12,14 @@
     </stdio>
     <command>
 <![CDATA[
-        ## 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
+        ## 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
 
         augustus
             --strand=$strand
             $noInFrameStop
             $gff
+            --uniqueGeneId=true
 
             #if 'protein' in str($outputs).split(','):
                 --protein=on
@@ -59,11 +59,10 @@
 
             $singlestrand
             $input_genome
-            $mea
             $utr
             --genemodel=$genemodel
             --species=$organism
-            ##--outfile=$output
+
         | tee $output
         #if 'protein' in str($outputs).split(',') or 'codingseq' in str($outputs).split(','):
             | python $__tool_directory__/extract_features.py
@@ -78,10 +77,19 @@
     </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 (--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="noInFrameStop" argument="--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. (--noInFrameStop)" />
+        <param name="singlestrand" type="boolean" argument="--singlestrand"
+            label="Predict genes independently on each strand"
+            help="This allows overlapping genes on opposite strands. (--singlestrand)"
+            truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" />
+
+        <param name="utr" type="boolean" argument="--UTR"
+            label="Predict the untranslated regions in addition to the coding sequence"
+            truevalue="--UTR=on" falsevalue="--UTR=off" checked="false"
+            help="This currently works only for human, galdieria, toxoplasma and caenorhabditis. (--UTR)" />
 
         <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
             <option value="human">Homo sapiens</option>
@@ -94,7 +102,7 @@
             <option value="tetrahymena">Tetrahymena thermophila</option>
             <option value="galdieria">Galdieria sulphuraria</option>
             <option value="maize">Zea mays</option>
-            <option value="toxoplasma ">Toxoplasma gondii</option>
+            <option value="toxoplasma">Toxoplasma gondii</option>
             <option value="caenorhabditis ">Caenorhabditis elegans</option>
             <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
             <option value="aspergillus_nidulans ">Aspergillus nidulans</option>
@@ -105,18 +113,19 @@
             <option value="candida_guilliermondii ">Candida guilliermondii</option>
             <option value="candida_tropicalis ">Candida tropicalis</option>
             <option value="chaetomium_globosum">Chaetomium globosum</option>
-            <option value="coccidioides_immitis ">Coccidioides immitis</option>
-            <option value="coprinus ">Coprinus cinereus</option>
+            <option value="coccidioides_immitis">Coccidioides immitis</option>
+            <option value="coprinus">Coprinus cinereus</option>
             <option value="coprinus_cinereus">Coprinus cinereus</option>
-            <option value="cryptococcus_neoformans_gattii ">Cryptococcus neoformans gattii</option>
-            <option value="cryptococcus_neoformans_neoformans_B ">Cryptococcus neoformans neoformans</option>
-            <option value="cryptococcus_neoformans_neoformans_JEC21 ">Cryptococcus neoformans neoformans</option>
+            <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
+            <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option>
+            <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option>
+            <option value="cryptococcus">Cryptococcus neoformans</option>
             <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
             <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
             <option value="eremothecium_gossypii">Eremothecium gossypii</option>
             <option value="fusarium_graminearum ">Fusarium graminearum</option>
             <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
-            <option value="(histoplasma)">Histoplasma capsulatum</option>
+            <option value="histoplasma">Histoplasma capsulatum</option>
             <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
             <option value="laccaria_bicolor ">Laccaria bicolor</option>
             <option value="lamprey">Petromyzon marinus</option>
@@ -127,9 +136,9 @@
             <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
             <option value="pichia_stipitis">Pichia stipitis</option>
             <option value="rhizopus_oryzae">Rhizopus oryzae</option>
-            <option value="saccharomyces_cerevisiae_S288C ">Saccharomyces cerevisiae</option>
-            <option value="saccharomyces_cerevisiae_rm11-1a_1 ">Saccharomyces cerevisiae</option>
-            <option value="(saccharomyces)">Saccharomyces cerevisiae</option>
+            <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option>
+            <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option>
+            <option value="saccharomyces">Saccharomyces cerevisiae</option>
             <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
             <option value="trichinella">Trichinella spiralis</option>
             <option value="ustilago_maydis">Ustilago maydis</option>
@@ -143,25 +152,62 @@
             <option value="cacao">Theobroma cacao (cacao)</option>
             <option value="heliconius_melpomene1">Heliconius melpomene</option>
             <option value="xenoturbella">Xenoturbella</option>
-        </param>
+            <option value="E_coli_K12">E coli K12</option>
+            <option value="c_elegans_trsk">c elegans trsk</option>
+            <option value="camponotus_floridanus">Camponotus floridanus</option>
+            <option value="coyote_tobacco">Coyote tobacco</option>
+            <option value="s_aureus">Staphylococcus aureus</option>
+            <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
+            <option value="wheat">wheat</option>
+            <option value="zebrafish">Danio rerio</option>
+            <option value="anidulans">Aspergillus nidulans</option>
+            <option value="bombus_impatiens1">Bombus impatiens1</option>
+            <option value="bombus_terrestris2">Bombus terrestris2</option>
+            <option value="botrytis_cinerea">Botrytis cinerea</option>
+            <option value="brugia_malayi">Brugia malayi</option>
+            <option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
+            <option value="cryptococcus_neoformans">Cryptococcus neoformans</option>
+            <option value="culex_pipiens">Culex pipiens</option>
+            <option value="elephant_shark">Callorhinchus milii</option>
+            <option value="honeybee1">Apis mellifera</option>
+            <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
+            <option value="pea_aphid">Acyrthosiphon pisum</option>
+            <option value="rhodnius_prolixus">Rhodnius prolixus</option>
+            <option value="ustilago_maydis">Ustilago maydis</option>
+            <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option>
+            <option value="verticillium_longisporum1">Verticillium longisporum1</option>
+            <option value="Xipophorus_maculatus">Xipophorus_maculatus</option>
+            <option value="adorsata">adorsata</option>
+            <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
+            <option value="maker2_athal1">maker2_athal1</option>
+            <option value="maker2_c_elegans1">maker2_c_elegans1</option>
+            <option value="maker2_dmel1">maker2_dmel1</option>
+            <option value="maker2_spomb1">maker2_spomb1</option>
+            <option value="parasteatoda">parasteatoda</option>
+            <option value="rice">rice</option>
+            <option value="schistosoma2">schistosoma2</option>
+            <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</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.">
+        <param name="strand" type="select" argument="--strand"
+            label="Predict genes on specific strands" help="(--strand)">
             <option value="both">both</option>
             <option value="forward">forward</option>
             <option value="backward">backward</option>
         </param>
 
-        <param name="genemodel" label="Gene Model" type="select" multiple="false" format="text" help="Gene Model to predict, for more information please refere to the help.">
+        <param name="genemodel" label="Gene Model" type="select"
+            help="Gene Model to predict, for more information please refere to the help. (--genemodel)">
             <option value="complete">complete</option>
             <option value="partial">partial</option>
             <option value="intronless">intronless</option>
             <option value="atleastone">atleastone</option>
             <option value="exactlyone">exactlyone</option>
-            <option value="bacterium">bacterium (beta version)</option>
         </param>
 
-
-        <param name="gff" type="boolean" label="GFF formated output, standard is GTF (--gff3)" truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
+        <param name="gff" type="boolean" label="GFF formated output"
+            help="Standard output is GTF. (--gff3)"
+            truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
 
         <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
             <option value="protein" selected="True">predicted protein sequences (--protein)</option>
@@ -174,12 +220,11 @@
             <validator type="no_options" message="Please select at least one output file." />
         </param>
 
-
     </inputs>
     <outputs>
         <data format="gtf" name="output" label="${tool.name} on ${on_string}: GTF/GFF">
             <change_format>
-                <when input="gff" value="--gff3=on" format="gff" />
+                <when input="gff" value="--gff3=on" format="gff3" />
             </change_format>
         </data>
         <data format="fasta" name="protein_output" label="${tool.name} on ${on_string}: Protein sequence">
@@ -193,28 +238,21 @@
         <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"/>
+            <param name="utr" value="True" />
+            <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="6"/>
         </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"/>
+            <param name="utr" value="True" />
+            <param name="gff" value="True" />
+            <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="6"/>
         </test>
         <test>
             <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
             <param name="organism" value="human" />
-            <param name="outputs" value="protein,codingseq,introns,cds" />
-            <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gff" lines_diff="2"/>
+            <param name="outputs" value="protein,codingseq,introns,cds,start,stop" />
+            <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gtf" lines_diff="6"/>
             <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>
diff -r a77a4e9921e0 -r f5075dee9d6b test-data/arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf
--- a/test-data/arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf	Wed May 06 14:31:02 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,85 +0,0 @@
-# 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
diff -r a77a4e9921e0 -r f5075dee9d6b test-data/human_augustus_protein_codingseq_introns_cds_codingseq.fasta
--- a/test-data/human_augustus_protein_codingseq_introns_cds_codingseq.fasta	Wed May 06 14:31:02 2015 -0400
+++ b/test-data/human_augustus_protein_codingseq_introns_cds_codingseq.fasta	Fri May 22 04:55:25 2015 -0400
@@ -1,4 +1,4 @@
->g1
+>HS04636.g1
 atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtca
 tgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtcaa
 aaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactg
@@ -23,7 +23,7 @@
 cacttttggtggagaagtgggttttcaaatcatcaacactgcctcaattcagtctctcatctgcaataacgtgaagggct
 gtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaagttcttcccgctccgga
 ctagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag
->g2
+>HS08198.g2
 atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccaca
 tgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccacgc
 cggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggc
diff -r a77a4e9921e0 -r f5075dee9d6b test-data/human_augustus_protein_codingseq_introns_cds_main.gtf
--- a/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf	Wed May 06 14:31:02 2015 -0400
+++ b/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf	Fri May 22 04:55:25 2015 -0400
@@ -1,13 +1,13 @@
-# 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).
+# This output was generated with AUGUSTUS (version 3.1.0).
+# AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de),
+# Oliver Keller, Stefanie König and Lizzy Gerischer.
 # 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 ...
+# Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ...
 # human version. Using default transition matrix.
-# Looks like /home/bag/projects/galaxy/galaxy-central/database/files/001/dataset_1149.dat is in fasta format.
+# Looks like /tmp/tmpboMLLQ/job_working_directory/000/6/task_0/dataset_9.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) -----
@@ -15,28 +15,30 @@
 # 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";
+# start gene HS04636.g1
+HS04636	AUGUSTUS	gene	966	6903	1	+	.	HS04636.g1
+HS04636	AUGUSTUS	transcript	966	6903	.	+	.	HS04636.g1.t1
+HS04636	AUGUSTUS	start_codon	966	968	.	+	0	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	intron	1018	1817	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	intron	1935	2054	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	intron	2199	2851	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	intron	2996	3425	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	intron	3608	4339	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	intron	4424	4542	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	intron	4790	5071	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	intron	5359	5859	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	intron	6008	6493	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	966	1017	.	+	0	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	1818	1934	.	+	2	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	2055	2198	.	+	2	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	2852	2995	.	+	2	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	3426	3607	.	+	2	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	4340	4423	.	+	0	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	4543	4789	.	+	0	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	5072	5358	.	+	2	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	5860	6007	.	+	0	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	6494	6903	.	+	2	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	stop_codon	6901	6903	.	+	0	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
 # coding sequence = [atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtc
 # aaaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccggaattt
 # ttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc
@@ -63,7 +65,7 @@
 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
 # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
-# end gene g1
+# end gene HS04636.g1
 ###
 #
 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
@@ -71,20 +73,22 @@
 # 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";
+# start gene HS08198.g2
+HS08198	AUGUSTUS	gene	445	1848	1	+	.	HS08198.g2
+HS08198	AUGUSTUS	transcript	445	1848	.	+	.	HS08198.g2.t1
+HS08198	AUGUSTUS	start_codon	445	447	.	+	0	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	intron	583	811	.	+	.	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	intron	895	1052	.	+	.	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	intron	1124	1207	.	+	.	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	intron	1316	1586	.	+	.	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	intron	1689	1771	.	+	.	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	CDS	445	582	.	+	0	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	CDS	812	894	.	+	0	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	CDS	1053	1123	.	+	1	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	CDS	1208	1315	.	+	2	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	CDS	1587	1688	.	+	2	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	CDS	1772	1848	.	+	2	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	stop_codon	1846	1848	.	+	0	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
 # coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac
 # gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg
 # gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg
@@ -95,7 +99,7 @@
 # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
 # HVLDGECTAGASMAAW]
-# end gene g2
+# end gene HS08198.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
+# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=on --start=on --stop=on --cds=on --singlestrand=false /tmp/tmpboMLLQ/job_working_directory/000/6/task_0/dataset_9.dat --UTR=off --genemodel=complete --species=human
diff -r a77a4e9921e0 -r f5075dee9d6b test-data/human_augustus_protein_codingseq_introns_cds_protein.fasta
--- a/test-data/human_augustus_protein_codingseq_introns_cds_protein.fasta	Wed May 06 14:31:02 2015 -0400
+++ b/test-data/human_augustus_protein_codingseq_introns_cds_protein.fasta	Fri May 22 04:55:25 2015 -0400
@@ -1,4 +1,4 @@
->g1
+>HS04636.g1
 MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILML
 ARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTHFK
 GFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNE
@@ -8,7 +8,7 @@
 HGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYG
 DIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCP
 FTSFSVPDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL
->g2
+>HS08198.g2
 MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICML
 PPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICWQVR
 QLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIF
diff -r a77a4e9921e0 -r f5075dee9d6b test-data/human_augustus_utr-on.gff
--- a/test-data/human_augustus_utr-on.gff	Wed May 06 14:31:02 2015 -0400
+++ b/test-data/human_augustus_utr-on.gff	Fri May 22 04:55:25 2015 -0400
@@ -1,46 +1,64 @@
 ##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).
+# This output was generated with AUGUSTUS (version 3.1.0).
+# AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de),
+# Oliver Keller, Stefanie König and Lizzy Gerischer.
 # 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.
+# Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ...
+# human version. Using default transition matrix.
+# Looks like /tmp/tmpboMLLQ/job_working_directory/000/4/task_0/dataset_5.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) -----
 #
 # 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
+# start gene HS04636.g1
+HS04636	AUGUSTUS	gene	836	8857	1	+	.	ID=HS04636.g1
+HS04636	AUGUSTUS	transcript	836	8857	.	+	.	ID=HS04636.g1.t1;Parent=HS04636.g1
+HS04636	AUGUSTUS	transcription_start_site	836	836	.	+	.	Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	exon	836	1017	.	+	.	Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	start_codon	966	968	.	+	0	Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	CDS	966	1017	.	+	0	ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	CDS	1818	1934	.	+	2	ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	exon	1818	1934	.	+	.	Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	CDS	2055	2198	.	+	2	ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	exon	2055	2198	.	+	.	Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	CDS	2852	2995	.	+	2	ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	exon	2852	2995	.	+	.	Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	CDS	3426	3607	.	+	2	ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	exon	3426	3607	.	+	.	Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	CDS	4340	4423	.	+	0	ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	exon	4340	4423	.	+	.	Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	CDS	4543	4789	.	+	0	ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	exon	4543	4789	.	+	.	Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	CDS	5072	5358	.	+	2	ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	exon	5072	5358	.	+	.	Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	CDS	5860	6007	.	+	0	ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	exon	5860	6007	.	+	.	Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	CDS	6494	6903	.	+	2	ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	exon	6494	8857	.	+	.	Parent=HS04636.g1.t1
+HS04636	AUGUSTUS	transcription_end_site	8857	8857	.	+	.	Parent=HS04636.g1.t1
+# 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
@@ -48,30 +66,41 @@
 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
 # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
-# end gene g1
+# end gene HS04636.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
+# start gene HS08198.g2
+HS08198	AUGUSTUS	gene	86	2105	1	+	.	ID=HS08198.g2
+HS08198	AUGUSTUS	transcript	86	2105	.	+	.	ID=HS08198.g2.t1;Parent=HS08198.g2
+HS08198	AUGUSTUS	transcription_start_site	86	86	.	+	.	Parent=HS08198.g2.t1
+HS08198	AUGUSTUS	exon	86	582	.	+	.	Parent=HS08198.g2.t1
+HS08198	AUGUSTUS	start_codon	445	447	.	+	0	Parent=HS08198.g2.t1
+HS08198	AUGUSTUS	CDS	445	582	.	+	0	ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
+HS08198	AUGUSTUS	CDS	812	894	.	+	0	ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
+HS08198	AUGUSTUS	exon	812	894	.	+	.	Parent=HS08198.g2.t1
+HS08198	AUGUSTUS	CDS	1053	1123	.	+	1	ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
+HS08198	AUGUSTUS	exon	1053	1123	.	+	.	Parent=HS08198.g2.t1
+HS08198	AUGUSTUS	CDS	1208	1315	.	+	2	ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
+HS08198	AUGUSTUS	exon	1208	1315	.	+	.	Parent=HS08198.g2.t1
+HS08198	AUGUSTUS	CDS	1587	1688	.	+	2	ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
+HS08198	AUGUSTUS	exon	1587	1688	.	+	.	Parent=HS08198.g2.t1
+HS08198	AUGUSTUS	CDS	1772	1848	.	+	2	ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
+HS08198	AUGUSTUS	exon	1772	2105	.	+	.	Parent=HS08198.g2.t1
+HS08198	AUGUSTUS	transcription_end_site	2105	2105	.	+	.	Parent=HS08198.g2.t1
+# coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac
+# gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg
+# gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg
+# ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg
+# cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact
+# gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc
+# ggcgtggtga]
 # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
-# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY]
-# end gene g2
+# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
+# HVLDGECTAGASMAAW]
+# end gene HS08198.g2
 ###
 # command line:
-# ./bin/augustus --species=human --UTR=on --gff3=on ./examples/example.fa
+# augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpboMLLQ/job_working_directory/000/4/task_0/dataset_5.dat --UTR=on --genemodel=complete --species=human
diff -r a77a4e9921e0 -r f5075dee9d6b test-data/human_augustus_utr-on.gtf
--- a/test-data/human_augustus_utr-on.gtf	Wed May 06 14:31:02 2015 -0400
+++ b/test-data/human_augustus_utr-on.gtf	Fri May 22 04:55:25 2015 -0400
@@ -1,13 +1,13 @@
-# 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).
+# This output was generated with AUGUSTUS (version 3.1.0).
+# AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de),
+# Oliver Keller, Stefanie König and Lizzy Gerischer.
 # 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.
+# Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ...
+# human version. Using default transition matrix.
+# Looks like /tmp/tmpboMLLQ/job_working_directory/000/2/task_0/dataset_1.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) -----
@@ -15,33 +15,51 @@
 # 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";
+# start gene HS04636.g1
+HS04636	AUGUSTUS	gene	836	8857	1	+	.	HS04636.g1
+HS04636	AUGUSTUS	transcript	836	8857	.	+	.	HS04636.g1.t1
+HS04636	AUGUSTUS	tss	836	836	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	exon	836	1017	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	start_codon	966	968	.	+	0	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	966	1017	.	+	0	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	1818	1934	.	+	2	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	exon	1818	1934	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	2055	2198	.	+	2	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	exon	2055	2198	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	2852	2995	.	+	2	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	exon	2852	2995	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	3426	3607	.	+	2	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	exon	3426	3607	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	4340	4423	.	+	0	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	exon	4340	4423	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	4543	4789	.	+	0	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	exon	4543	4789	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	5072	5358	.	+	2	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	exon	5072	5358	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	5860	6007	.	+	0	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	exon	5860	6007	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	CDS	6494	6903	.	+	2	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	exon	6494	8857	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636	AUGUSTUS	tts	8857	8857	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.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
@@ -49,7 +67,7 @@
 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
 # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
-# end gene g1
+# end gene HS04636.g1
 ###
 #
 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
@@ -57,24 +75,35 @@
 # 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";
+# start gene HS08198.g2
+HS08198	AUGUSTUS	gene	86	2105	1	+	.	HS08198.g2
+HS08198	AUGUSTUS	transcript	86	2105	.	+	.	HS08198.g2.t1
+HS08198	AUGUSTUS	tss	86	86	.	+	.	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	exon	86	582	.	+	.	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	start_codon	445	447	.	+	0	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	CDS	445	582	.	+	0	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	CDS	812	894	.	+	0	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	exon	812	894	.	+	.	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	CDS	1053	1123	.	+	1	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	exon	1053	1123	.	+	.	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	CDS	1208	1315	.	+	2	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	exon	1208	1315	.	+	.	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	CDS	1587	1688	.	+	2	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	exon	1587	1688	.	+	.	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	CDS	1772	1848	.	+	2	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	exon	1772	2105	.	+	.	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198	AUGUSTUS	tts	2105	2105	.	+	.	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+# coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac
+# gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg
+# gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg
+# ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg
+# cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact
+# gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc
+# ggcgtggtga]
 # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
-# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY]
-# end gene g2
+# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
+# HVLDGECTAGASMAAW]
+# end gene HS08198.g2
 ###
 # command line:
-# ./bin/augustus --species=human --UTR=on ./examples/example.fa
+# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpboMLLQ/job_working_directory/000/2/task_0/dataset_1.dat --UTR=on --genemodel=complete --species=human
diff -r a77a4e9921e0 -r f5075dee9d6b tool_conf.xml
--- a/tool_conf.xml	Wed May 06 14:31:02 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<toolbox>
-  <section name="Gene Prediction" id="gene_prediction">
-        <tool file="gene_prediction/tools/augustus/augustus.xml" />
-  </section>
-</toolbox>
diff -r a77a4e9921e0 -r f5075dee9d6b tool_dependencies.xml
--- a/tool_dependencies.xml	Wed May 06 14:31:02 2015 -0400
+++ b/tool_dependencies.xml	Fri May 22 04:55:25 2015 -0400
@@ -1,33 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="augustus" version="2.7">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus.2.7.tar.gz</action>
-                <action type="shell_command">make</action>
-                <action type="move_directory_files">
-                    <source_directory>bin</source_directory>
-                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
-                </action>
-                <action type="move_directory_files">
-                    <source_directory>scripts</source_directory>
-                    <destination_directory>$INSTALL_DIR/scripts</destination_directory>
-                </action>
-                <action type="move_directory_files">
-                    <source_directory>config</source_directory>
-                    <destination_directory>$INSTALL_DIR/config</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable name="AUGUSTUS_CONFIG_PATH" action="set_to">$INSTALL_DIR/config</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <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 name="augustus" version="3.1">
+        <repository changeset_revision="cc0bd4986b48" name="package_augustus_3_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>