| Previous changeset 2:a77a4e9921e0 (2015-05-06) Next changeset 4:4de31938431b (2017-10-20) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac |
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modified:
augustus.xml 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 |
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removed:
test-data/arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf tool_conf.xml |
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| 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 |
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| b'@@ -1,8 +1,8 @@\n-<tool id="augustus" name="Augustus" version="0.3.1">\n+<tool id="augustus" name="Augustus" version="3.1.0">\n <description>gene prediction for eukaryotic genomes</description>\n <parallelism method="multi" split_inputs="input_genome" split_mode="to_size" split_size="10" merge_outputs="output,protein_output,codingseq_output"></parallelism>\n <requirements>\n- <requirement type="package" version="2.7">augustus</requirement>\n+ <requirement type="package" version="3.1">augustus</requirement>\n </requirements>\n <stdio>\n <exit_code range="1:" />\n@@ -12,14 +12,14 @@\n </stdio>\n <command>\n <![CDATA[\n- ## please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config\n- ## or use the --AUGUSTUS_CONFIG_PATH=path if you are not installing through the toolshed\n- ## 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\n+ ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external\n+ ## script is used to extract the sequences into additional files\n \n augustus\n --strand=$strand\n $noInFrameStop\n $gff\n+ --uniqueGeneId=true\n \n #if \'protein\' in str($outputs).split(\',\'):\n --protein=on\n@@ -59,11 +59,10 @@\n \n $singlestrand\n $input_genome\n- $mea\n $utr\n --genemodel=$genemodel\n --species=$organism\n- ##--outfile=$output\n+\n | tee $output\n #if \'protein\' in str($outputs).split(\',\') or \'codingseq\' in str($outputs).split(\',\'):\n | python $__tool_directory__/extract_features.py\n@@ -78,10 +77,19 @@\n </command>\n <inputs>\n <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>\n- <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" />\n- <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" />\n- <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." />\n- <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." />\n+ <param name="noInFrameStop" argument="--noInFrameStop" type="boolean"\n+ label="Don\'t report transcripts with in-frame stop codons (--noInFrameStop)"\n+ truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false"\n+ help="Otherwise, intron-spanning stop codons could occur. (--noInFrameStop)" />\n+ <param name="singlestrand" type="boolean" argument="--singlestrand"\n+ label="Predict genes independently on each strand"\n+ help="This allows overlapping genes on opposite strands. (--singlestrand)"\n+ truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" />\n+\n+ <param name="utr" type="boolean" argument="--UTR"\n+ label="Predict the untranslated regions in addition to the coding sequence"\n+ truevalue="--UTR=on" falsevalue="--UTR=off" checked="false"\n+ help="This currently works only for human, galdieria, toxoplasma and caenorhabditis. (--UTR)" />\n \n <param name="organism" la'..b'enemodel" label="Gene Model" type="select"\n+ help="Gene Model to predict, for more information please refere to the help. (--genemodel)">\n <option value="complete">complete</option>\n <option value="partial">partial</option>\n <option value="intronless">intronless</option>\n <option value="atleastone">atleastone</option>\n <option value="exactlyone">exactlyone</option>\n- <option value="bacterium">bacterium (beta version)</option>\n </param>\n \n-\n- <param name="gff" type="boolean" label="GFF formated output, standard is GTF (--gff3)" truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />\n+ <param name="gff" type="boolean" label="GFF formated output"\n+ help="Standard output is GTF. (--gff3)"\n+ truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />\n \n <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">\n <option value="protein" selected="True">predicted protein sequences (--protein)</option>\n@@ -174,12 +220,11 @@\n <validator type="no_options" message="Please select at least one output file." />\n </param>\n \n-\n </inputs>\n <outputs>\n <data format="gtf" name="output" label="${tool.name} on ${on_string}: GTF/GFF">\n <change_format>\n- <when input="gff" value="--gff3=on" format="gff" />\n+ <when input="gff" value="--gff3=on" format="gff3" />\n </change_format>\n </data>\n <data format="fasta" name="protein_output" label="${tool.name} on ${on_string}: Protein sequence">\n@@ -193,28 +238,21 @@\n <test>\n <param name="input_genome" value="human_augustus.fa" ftype="fasta" />\n <param name="organism" value="human" />\n- <param name="utr" value="--UTR=on" />\n- <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="2"/>\n+ <param name="utr" value="True" />\n+ <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="6"/>\n </test>\n <test>\n <param name="input_genome" value="human_augustus.fa" ftype="fasta" />\n <param name="organism" value="human" />\n- <param name="utr" value="--UTR=on" />\n- <param name="gff" value="--gff3=on" />\n- <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="2"/>\n- </test>\n- <test>\n- <param name="input_genome" value="arabidopsis_augustus.fa" ftype="fasta" />\n- <param name="organism" value="arabidopsis" />\n- <param name="singlestrand" value="--singlestrand=true" />\n- <param name="mea" value="--mea=1" />\n- <output name="output" file="arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf" ftype="gtf" lines_diff="2"/>\n+ <param name="utr" value="True" />\n+ <param name="gff" value="True" />\n+ <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="6"/>\n </test>\n <test>\n <param name="input_genome" value="human_augustus.fa" ftype="fasta" />\n <param name="organism" value="human" />\n- <param name="outputs" value="protein,codingseq,introns,cds" />\n- <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gff" lines_diff="2"/>\n+ <param name="outputs" value="protein,codingseq,introns,cds,start,stop" />\n+ <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gtf" lines_diff="6"/>\n <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" />\n <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />\n </test>\n' |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -1,4 +1,4 @@ ->g1 +>HS04636.g1 atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtca tgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtcaa aaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactg @@ -23,7 +23,7 @@ cacttttggtggagaagtgggttttcaaatcatcaacactgcctcaattcagtctctcatctgcaataacgtgaagggct gtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaagttcttcccgctccgga ctagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag ->g2 +>HS08198.g2 atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccaca tgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccacgc cggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggc |
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| 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 |
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| b'@@ -1,13 +1,13 @@\n-# This output was generated with AUGUSTUS (version 2.7).\n-# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.de)\n-# and Oliver Keller (keller@cs.uni-goettingen.de).\n+# This output was generated with AUGUSTUS (version 3.1.0).\n+# AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de),\n+# Oliver Keller, Stefanie K\xc3\xb6nig and Lizzy Gerischer.\n # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),\n # Using native and syntenically mapped cDNA alignments to improve de novo gene finding\n # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013\n # No extrinsic information on sequences given.\n-# Initialising the parameters ...\n+# Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ...\n # human version. Using default transition matrix.\n-# Looks like /home/bag/projects/galaxy/galaxy-central/database/files/001/dataset_1149.dat is in fasta format.\n+# Looks like /tmp/tmpboMLLQ/job_working_directory/000/6/task_0/dataset_9.dat is in fasta format.\n # We have hints for 0 sequences and for 0 of the sequences in the input set.\n #\n # ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----\n@@ -15,28 +15,30 @@\n # Constraints/Hints:\n # (none)\n # Predicted genes for sequence number 1 on both strands\n-# start gene g1\n-HS04636\tAUGUSTUS\tgene\t966\t6903\t1\t+\t.\tg1\n-HS04636\tAUGUSTUS\ttranscript\t966\t6903\t.\t+\t.\tg1.t1\n-HS04636\tAUGUSTUS\tintron\t1018\t1817\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tintron\t1935\t2054\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tintron\t2199\t2851\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tintron\t2996\t3425\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tintron\t3608\t4339\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tintron\t4424\t4542\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tintron\t4790\t5071\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tintron\t5359\t5859\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tintron\t6008\t6493\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t966\t1017\t.\t+\t0\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t1818\t1934\t.\t+\t2\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t2055\t2198\t.\t+\t2\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t2852\t2995\t.\t+\t2\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t3426\t3607\t.\t+\t2\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t4340\t4423\t.\t+\t0\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t4543\t4789\t.\t+\t0\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t5072\t5358\t.\t+\t2\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t5860\t6007\t.\t+\t0\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t6494\t6903\t.\t+\t2\ttranscript_id "g1.t1"; gene_id "g1";\n+# start gene HS04636.g1\n+HS04636\tAUGUSTUS\tgene\t966\t6903\t1\t+\t.\tHS04636.g1\n+HS04636\tAUGUSTUS\ttranscript\t966\t6903\t.\t+\t.\tHS04636.g1.t1\n+HS04636\tAUGUSTUS\tstart_codon\t966\t968\t.\t+\t0\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tintron\t1018\t1817\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tintron\t1935\t2054\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tintron\t2199\t2851\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tintron\t2996\t3425\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tintron\t3608\t4339\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tintron\t4424\t4542\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tintron\t4790\t5071\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tintron\t5359\t5859\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+H'..b'gtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc\n@@ -63,7 +65,7 @@\n # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE\n # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV\n # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]\n-# end gene g1\n+# end gene HS04636.g1\n ###\n #\n # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----\n@@ -71,20 +73,22 @@\n # Constraints/Hints:\n # (none)\n # Predicted genes for sequence number 2 on both strands\n-# start gene g2\n-HS08198\tAUGUSTUS\tgene\t445\t1848\t1\t+\t.\tg2\n-HS08198\tAUGUSTUS\ttranscript\t445\t1848\t.\t+\t.\tg2.t1\n-HS08198\tAUGUSTUS\tintron\t583\t811\t.\t+\t.\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\tintron\t895\t1052\t.\t+\t.\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\tintron\t1124\t1207\t.\t+\t.\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\tintron\t1316\t1586\t.\t+\t.\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\tintron\t1689\t1771\t.\t+\t.\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\tCDS\t445\t582\t.\t+\t0\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\tCDS\t812\t894\t.\t+\t0\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\tCDS\t1053\t1123\t.\t+\t1\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\tCDS\t1208\t1315\t.\t+\t2\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\tCDS\t1587\t1688\t.\t+\t2\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\tCDS\t1772\t1848\t.\t+\t2\ttranscript_id "g2.t1"; gene_id "g2";\n+# start gene HS08198.g2\n+HS08198\tAUGUSTUS\tgene\t445\t1848\t1\t+\t.\tHS08198.g2\n+HS08198\tAUGUSTUS\ttranscript\t445\t1848\t.\t+\t.\tHS08198.g2.t1\n+HS08198\tAUGUSTUS\tstart_codon\t445\t447\t.\t+\t0\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tintron\t583\t811\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tintron\t895\t1052\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tintron\t1124\t1207\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tintron\t1316\t1586\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tintron\t1689\t1771\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t445\t582\t.\t+\t0\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t812\t894\t.\t+\t0\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t1053\t1123\t.\t+\t1\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t1208\t1315\t.\t+\t2\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t1587\t1688\t.\t+\t2\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t1772\t1848\t.\t+\t2\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tstop_codon\t1846\t1848\t.\t+\t0\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n # coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac\n # gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg\n # gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg\n@@ -95,7 +99,7 @@\n # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC\n # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF\n # HVLDGECTAGASMAAW]\n-# end gene g2\n+# end gene HS08198.g2\n ###\n # command line:\n-# 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\n+# 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\n' |
| b |
| 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 |
| b |
| @@ -1,4 +1,4 @@ ->g1 +>HS04636.g1 MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILML ARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTHFK GFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNE @@ -8,7 +8,7 @@ HGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYG DIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCP FTSFSVPDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL ->g2 +>HS08198.g2 MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICML PPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICWQVR QLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIF |
| b |
| 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 |
| [ |
| b'@@ -1,46 +1,64 @@\n ##gff-version 3\n-# This output was generated with AUGUSTUS (version 2.7).\n-# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.de)\n-# and Oliver Keller (keller@cs.uni-goettingen.de).\n+# This output was generated with AUGUSTUS (version 3.1.0).\n+# AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de),\n+# Oliver Keller, Stefanie K\xc3\xb6nig and Lizzy Gerischer.\n # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),\n # Using native and syntenically mapped cDNA alignments to improve de novo gene finding\n # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013\n # No extrinsic information on sequences given.\n-# Initialising the parameters ...\n-# human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl\n-# Looks like ./examples/example.fa is in fasta format.\n+# Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ...\n+# human version. Using default transition matrix.\n+# Looks like /tmp/tmpboMLLQ/job_working_directory/000/4/task_0/dataset_5.dat is in fasta format.\n # We have hints for 0 sequences and for 0 of the sequences in the input set.\n #\n # ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----\n #\n # Predicted genes for sequence number 1 on both strands\n-# start gene g1\n-HS04636\tAUGUSTUS\tgene\t836\t8857\t1\t+\t.\tID=g1\n-HS04636\tAUGUSTUS\ttranscript\t836\t8857\t.\t+\t.\tID=g1.t1;Parent=g1\n-HS04636\tAUGUSTUS\ttranscription_start_site\t836\t836\t.\t+\t.\tParent=g1.t1\n-HS04636\tAUGUSTUS\texon\t836\t1017\t.\t+\t.\tParent=g1.t1\n-HS04636\tAUGUSTUS\tstart_codon\t966\t968\t.\t+\t0\tParent=g1.t1\n-HS04636\tAUGUSTUS\tCDS\t966\t1017\t.\t+\t0\tID=g1.t1.cds;Parent=g1.t1\n-HS04636\tAUGUSTUS\tCDS\t1818\t1934\t.\t+\t2\tID=g1.t1.cds;Parent=g1.t1\n-HS04636\tAUGUSTUS\texon\t1818\t1934\t.\t+\t.\tParent=g1.t1\n-HS04636\tAUGUSTUS\tCDS\t2055\t2198\t.\t+\t2\tID=g1.t1.cds;Parent=g1.t1\n-HS04636\tAUGUSTUS\texon\t2055\t2198\t.\t+\t.\tParent=g1.t1\n-HS04636\tAUGUSTUS\tCDS\t2852\t2995\t.\t+\t2\tID=g1.t1.cds;Parent=g1.t1\n-HS04636\tAUGUSTUS\texon\t2852\t2995\t.\t+\t.\tParent=g1.t1\n-HS04636\tAUGUSTUS\tCDS\t3426\t3607\t.\t+\t2\tID=g1.t1.cds;Parent=g1.t1\n-HS04636\tAUGUSTUS\texon\t3426\t3607\t.\t+\t.\tParent=g1.t1\n-HS04636\tAUGUSTUS\tCDS\t4340\t4423\t.\t+\t0\tID=g1.t1.cds;Parent=g1.t1\n-HS04636\tAUGUSTUS\texon\t4340\t4423\t.\t+\t.\tParent=g1.t1\n-HS04636\tAUGUSTUS\tCDS\t4543\t4789\t.\t+\t0\tID=g1.t1.cds;Parent=g1.t1\n-HS04636\tAUGUSTUS\texon\t4543\t4789\t.\t+\t.\tParent=g1.t1\n-HS04636\tAUGUSTUS\tCDS\t5072\t5358\t.\t+\t2\tID=g1.t1.cds;Parent=g1.t1\n-HS04636\tAUGUSTUS\texon\t5072\t5358\t.\t+\t.\tParent=g1.t1\n-HS04636\tAUGUSTUS\tCDS\t5860\t6007\t.\t+\t0\tID=g1.t1.cds;Parent=g1.t1\n-HS04636\tAUGUSTUS\texon\t5860\t6007\t.\t+\t.\tParent=g1.t1\n-HS04636\tAUGUSTUS\tCDS\t6494\t6903\t.\t+\t2\tID=g1.t1.cds;Parent=g1.t1\n-HS04636\tAUGUSTUS\texon\t6494\t8857\t.\t+\t.\tParent=g1.t1\n-HS04636\tAUGUSTUS\tstop_codon\t6901\t6903\t.\t+\t0\tParent=g1.t1\n-HS04636\tAUGUSTUS\ttranscription_end_site\t8857\t8857\t.\t+\t.\tParent=g1.t1\n+# start gene HS04636.g1\n+HS04636\tAUGUSTUS\tgene\t836\t8857\t1\t+\t.\tID=HS04636.g1\n+HS04636\tAUGUSTUS\ttranscript\t836\t8857\t.\t+\t.\tID=HS04636.g1.t1;Parent=HS04636.g1\n+HS04636\tAUGUSTUS\ttranscription_start_site\t836\t836\t.\t+\t.\tParent=HS04636.g1.t1\n+HS04636\tAUGUSTUS\texon\t836\t1017\t.\t+\t.\tParent=HS04636.g1.t1\n+HS04636\tAUGUSTUS\tstart_codon\t966\t968\t.\t+\t0\tParent=HS04636.g1.t1\n+HS04636\tAUGUSTUS\tCDS\t966\t1017\t.\t+\t0\tID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1\n+HS04636\tAUGUSTUS\tCDS\t1818\t1934\t.\t+\t2\tID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1\n+HS04636\tAUGUSTUS\texon\t1818\t1934\t.\t+\t.\tParent=HS04636.g1.t1\n+HS04636\tAUGUSTUS\tCDS\t2055\t2198\t.\t+\t2\tID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1\n+HS04636\tAUGUSTUS\texon\t2055\t2198\t.\t+\t.\tParent=HS04636.g1.t1\n+HS04636\tAUGUSTUS\tCDS\t2852\t2995\t.\t+\t2\tID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1\n+HS04636\tAUGUSTUS\texon\t2852\t2995\t.\t+\t.\tParent=HS04636.g1.t1\n+HS04636\tAUGUSTUS\tCDS\t3426\t3607\t.\t+\t2\tID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1\n+HS046'..b'YNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD\n # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG\n@@ -48,30 +66,41 @@\n # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE\n # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV\n # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]\n-# end gene g1\n+# end gene HS04636.g1\n ###\n #\n # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----\n #\n # Predicted genes for sequence number 2 on both strands\n-# start gene g2\n-HS08198\tAUGUSTUS\tgene\t86\t2344\t1\t+\t.\tID=g2\n-HS08198\tAUGUSTUS\ttranscript\t86\t2344\t.\t+\t.\tID=g2.t1;Parent=g2\n-HS08198\tAUGUSTUS\ttranscription_start_site\t86\t86\t.\t+\t.\tParent=g2.t1\n-HS08198\tAUGUSTUS\texon\t86\t582\t.\t+\t.\tParent=g2.t1\n-HS08198\tAUGUSTUS\tstart_codon\t445\t447\t.\t+\t0\tParent=g2.t1\n-HS08198\tAUGUSTUS\tCDS\t445\t582\t.\t+\t0\tID=g2.t1.cds;Parent=g2.t1\n-HS08198\tAUGUSTUS\tCDS\t812\t894\t.\t+\t0\tID=g2.t1.cds;Parent=g2.t1\n-HS08198\tAUGUSTUS\texon\t812\t894\t.\t+\t.\tParent=g2.t1\n-HS08198\tAUGUSTUS\tCDS\t1053\t1123\t.\t+\t1\tID=g2.t1.cds;Parent=g2.t1\n-HS08198\tAUGUSTUS\texon\t1053\t1123\t.\t+\t.\tParent=g2.t1\n-HS08198\tAUGUSTUS\tCDS\t1208\t1315\t.\t+\t2\tID=g2.t1.cds;Parent=g2.t1\n-HS08198\tAUGUSTUS\texon\t1208\t1315\t.\t+\t.\tParent=g2.t1\n-HS08198\tAUGUSTUS\tCDS\t1587\t1688\t.\t+\t2\tID=g2.t1.cds;Parent=g2.t1\n-HS08198\tAUGUSTUS\texon\t1587\t1688\t.\t+\t.\tParent=g2.t1\n+# start gene HS08198.g2\n+HS08198\tAUGUSTUS\tgene\t86\t2105\t1\t+\t.\tID=HS08198.g2\n+HS08198\tAUGUSTUS\ttranscript\t86\t2105\t.\t+\t.\tID=HS08198.g2.t1;Parent=HS08198.g2\n+HS08198\tAUGUSTUS\ttranscription_start_site\t86\t86\t.\t+\t.\tParent=HS08198.g2.t1\n+HS08198\tAUGUSTUS\texon\t86\t582\t.\t+\t.\tParent=HS08198.g2.t1\n+HS08198\tAUGUSTUS\tstart_codon\t445\t447\t.\t+\t0\tParent=HS08198.g2.t1\n+HS08198\tAUGUSTUS\tCDS\t445\t582\t.\t+\t0\tID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1\n+HS08198\tAUGUSTUS\tCDS\t812\t894\t.\t+\t0\tID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1\n+HS08198\tAUGUSTUS\texon\t812\t894\t.\t+\t.\tParent=HS08198.g2.t1\n+HS08198\tAUGUSTUS\tCDS\t1053\t1123\t.\t+\t1\tID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1\n+HS08198\tAUGUSTUS\texon\t1053\t1123\t.\t+\t.\tParent=HS08198.g2.t1\n+HS08198\tAUGUSTUS\tCDS\t1208\t1315\t.\t+\t2\tID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1\n+HS08198\tAUGUSTUS\texon\t1208\t1315\t.\t+\t.\tParent=HS08198.g2.t1\n+HS08198\tAUGUSTUS\tCDS\t1587\t1688\t.\t+\t2\tID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1\n+HS08198\tAUGUSTUS\texon\t1587\t1688\t.\t+\t.\tParent=HS08198.g2.t1\n+HS08198\tAUGUSTUS\tCDS\t1772\t1848\t.\t+\t2\tID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1\n+HS08198\tAUGUSTUS\texon\t1772\t2105\t.\t+\t.\tParent=HS08198.g2.t1\n+HS08198\tAUGUSTUS\ttranscription_end_site\t2105\t2105\t.\t+\t.\tParent=HS08198.g2.t1\n+# coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac\n+# gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg\n+# gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg\n+# ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg\n+# cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact\n+# gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc\n+# ggcgtggtga]\n # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC\n-# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY]\n-# end gene g2\n+# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF\n+# HVLDGECTAGASMAAW]\n+# end gene HS08198.g2\n ###\n # command line:\n-# ./bin/augustus --species=human --UTR=on --gff3=on ./examples/example.fa\n+# 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\n' |
| b |
| 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 |
| [ |
| b'@@ -1,13 +1,13 @@\n-# This output was generated with AUGUSTUS (version 2.7).\n-# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.de)\n-# and Oliver Keller (keller@cs.uni-goettingen.de).\n+# This output was generated with AUGUSTUS (version 3.1.0).\n+# AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de),\n+# Oliver Keller, Stefanie K\xc3\xb6nig and Lizzy Gerischer.\n # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),\n # Using native and syntenically mapped cDNA alignments to improve de novo gene finding\n # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013\n # No extrinsic information on sequences given.\n-# Initialising the parameters ...\n-# human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl\n-# Looks like ./examples/example.fa is in fasta format.\n+# Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ...\n+# human version. Using default transition matrix.\n+# Looks like /tmp/tmpboMLLQ/job_working_directory/000/2/task_0/dataset_1.dat is in fasta format.\n # We have hints for 0 sequences and for 0 of the sequences in the input set.\n #\n # ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----\n@@ -15,33 +15,51 @@\n # Constraints/Hints:\n # (none)\n # Predicted genes for sequence number 1 on both strands\n-# start gene g1\n-HS04636\tAUGUSTUS\tgene\t836\t8857\t1\t+\t.\tg1\n-HS04636\tAUGUSTUS\ttranscript\t836\t8857\t.\t+\t.\tg1.t1\n-HS04636\tAUGUSTUS\ttss\t836\t836\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\texon\t836\t1017\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tstart_codon\t966\t968\t.\t+\t0\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t966\t1017\t.\t+\t0\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t1818\t1934\t.\t+\t2\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\texon\t1818\t1934\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t2055\t2198\t.\t+\t2\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\texon\t2055\t2198\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t2852\t2995\t.\t+\t2\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\texon\t2852\t2995\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t3426\t3607\t.\t+\t2\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\texon\t3426\t3607\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t4340\t4423\t.\t+\t0\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\texon\t4340\t4423\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t4543\t4789\t.\t+\t0\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\texon\t4543\t4789\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t5072\t5358\t.\t+\t2\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\texon\t5072\t5358\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t5860\t6007\t.\t+\t0\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\texon\t5860\t6007\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tCDS\t6494\t6903\t.\t+\t2\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\texon\t6494\t8857\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\tstop_codon\t6901\t6903\t.\t+\t0\ttranscript_id "g1.t1"; gene_id "g1";\n-HS04636\tAUGUSTUS\ttts\t8857\t8857\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n+# start gene HS04636.g1\n+HS04636\tAUGUSTUS\tgene\t836\t8857\t1\t+\t.\tHS04636.g1\n+HS04636\tAUGUSTUS\ttranscript\t836\t8857\t.\t+\t.\tHS04636.g1.t1\n+HS04636\tAUGUSTUS\ttss\t836\t836\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\texon\t836\t1017\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tstart_codon\t966\t968\t.\t+\t0\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t966\t1017\t.\t+\t0\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t'..b'(length = 2344, name = HS08198) -----\n@@ -57,24 +75,35 @@\n # Constraints/Hints:\n # (none)\n # Predicted genes for sequence number 2 on both strands\n-# start gene g2\n-HS08198\tAUGUSTUS\tgene\t86\t2344\t1\t+\t.\tg2\n-HS08198\tAUGUSTUS\ttranscript\t86\t2344\t.\t+\t.\tg2.t1\n-HS08198\tAUGUSTUS\ttss\t86\t86\t.\t+\t.\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\texon\t86\t582\t.\t+\t.\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\tstart_codon\t445\t447\t.\t+\t0\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\tCDS\t445\t582\t.\t+\t0\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\tCDS\t812\t894\t.\t+\t0\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\texon\t812\t894\t.\t+\t.\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\tCDS\t1053\t1123\t.\t+\t1\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\texon\t1053\t1123\t.\t+\t.\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\tCDS\t1208\t1315\t.\t+\t2\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\texon\t1208\t1315\t.\t+\t.\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\tCDS\t1587\t1688\t.\t+\t2\ttranscript_id "g2.t1"; gene_id "g2";\n-HS08198\tAUGUSTUS\texon\t1587\t1688\t.\t+\t.\ttranscript_id "g2.t1"; gene_id "g2";\n+# start gene HS08198.g2\n+HS08198\tAUGUSTUS\tgene\t86\t2105\t1\t+\t.\tHS08198.g2\n+HS08198\tAUGUSTUS\ttranscript\t86\t2105\t.\t+\t.\tHS08198.g2.t1\n+HS08198\tAUGUSTUS\ttss\t86\t86\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\texon\t86\t582\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tstart_codon\t445\t447\t.\t+\t0\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t445\t582\t.\t+\t0\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t812\t894\t.\t+\t0\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\texon\t812\t894\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t1053\t1123\t.\t+\t1\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\texon\t1053\t1123\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t1208\t1315\t.\t+\t2\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\texon\t1208\t1315\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t1587\t1688\t.\t+\t2\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\texon\t1587\t1688\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t1772\t1848\t.\t+\t2\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\texon\t1772\t2105\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\ttts\t2105\t2105\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+# coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac\n+# gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg\n+# gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg\n+# ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg\n+# cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact\n+# gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc\n+# ggcgtggtga]\n # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC\n-# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY]\n-# end gene g2\n+# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF\n+# HVLDGECTAGASMAAW]\n+# end gene HS08198.g2\n ###\n # command line:\n-# ./bin/augustus --species=human --UTR=on ./examples/example.fa\n+# 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\n' |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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> |