Mercurial > repos > bgruening > augustus_training
changeset 9:2fdc599f2814 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
| author | iuc |
|---|---|
| date | Thu, 17 Jul 2025 09:06:11 +0000 |
| parents | aada0deea587 |
| children | |
| files | augustus_training.xml macros.xml test-data/augustus.hints.output.gtf test-data/augustus.hints_and_range.output.gtf test-data/human_augustus.fa.gz test-data/human_augustus_protein_codingseq_introns_cds_main.gtf test-data/human_augustus_utr-on.gff test-data/human_augustus_utr-on.gtf test-data/human_augustus_utr-on_softmasking.gtf |
| diffstat | 9 files changed, 30 insertions(+), 35 deletions(-) [+] |
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--- a/augustus_training.xml Sun Dec 15 09:09:49 2024 +0000 +++ b/augustus_training.xml Thu Jul 17 09:06:11 2025 +0000 @@ -8,7 +8,7 @@ <xref type="bio.tools">augustus</xref> </xrefs> <expand macro="requirements"> - <requirement type="package" version="2.31.10">maker</requirement> + <requirement type="package" version="3.01.03">maker</requirement> </expand> <command><![CDATA[ cp -r `command -v augustus | xargs dirname`/../config/ augustus_dir/ &&
--- a/macros.xml Sun Dec 15 09:09:49 2024 +0000 +++ b/macros.xml Thu Jul 17 09:06:11 2025 +0000 @@ -7,8 +7,8 @@ </requirements> </xml> - <token name="@TOOL_VERSION@">3.4.0</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@TOOL_VERSION@">3.5.0</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">23.1</token>
--- a/test-data/augustus.hints.output.gtf Sun Dec 15 09:09:49 2024 +0000 +++ b/test-data/augustus.hints.output.gtf Thu Jul 17 09:06:11 2025 +0000 @@ -1,17 +1,17 @@ -# This output was generated with AUGUSTUS (version 3.4.0). +# This output was generated with AUGUSTUS (version 3.5.0). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), -# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. +# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. # 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 # Sources of extrinsic information: M RM E W # Setting CDSpart local malus: 0.985 # Setting UTRpart local malus: 0.973 -# reading in the file /tmp/tmpb49zmbej/files/6/4/3/dataset_64360fd3-ce82-407d-a499-79ac51decbd9.dat ... +# reading in the file /tmp/tmpjsgft19_/files/a/6/2/dataset_a62f021d-9ecd-4331-83ac-119ad4aac229.dat ... # Have extrinsic information about 1 sequences (in the specified range). # Initializing the parameters using config directory /usr/local/config/ ... # fly version. Using default transition matrix. -# Looks like /tmp/tmpb49zmbej/files/0/c/6/dataset_0c6b001d-370e-42cf-be92-b3435bd212c5.dat is in fasta format. +# Looks like /tmp/tmpjsgft19_/files/7/b/a/dataset_7ba46cfd-42e9-4f8e-8875-e339c6728906.dat is in fasta format. # We have hints for 1 sequence and for 1 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 9950, name = chr2R) ----- @@ -44,7 +44,6 @@ # start gene chr2R.g1 chr2R AUGUSTUS gene 7560 9303 0.84 - . chr2R.g1 chr2R AUGUSTUS transcript 7560 9303 0.84 - . chr2R.g1.t1 -chr2R AUGUSTUS start_codon 9301 9303 . - 0 transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1"; # Evidence for and against this transcript: # % of transcript supported by hints (any source): 57.1 # CDS exons: 4/4 @@ -59,4 +58,4 @@ # end gene chr2R.g1 ### # command line: -# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /tmp/tmpb49zmbej/files/0/c/6/dataset_0c6b001d-370e-42cf-be92-b3435bd212c5.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmpb49zmbej/files/6/4/3/dataset_64360fd3-ce82-407d-a499-79ac51decbd9.dat --extrinsicCfgFile=/tmp/tmpb49zmbej/files/8/6/b/dataset_86b0a149-1d37-4615-9915-2c48586e3ca1.dat --species=fly +# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --start=off --stop=off --cds=off --singlestrand=false /tmp/tmpjsgft19_/files/7/b/a/dataset_7ba46cfd-42e9-4f8e-8875-e339c6728906.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmpjsgft19_/files/a/6/2/dataset_a62f021d-9ecd-4331-83ac-119ad4aac229.dat --extrinsicCfgFile=/tmp/tmpjsgft19_/files/3/4/e/dataset_34e31244-f096-4c30-9f0d-5ca9e518e4bb.dat --species=fly
--- a/test-data/augustus.hints_and_range.output.gtf Sun Dec 15 09:09:49 2024 +0000 +++ b/test-data/augustus.hints_and_range.output.gtf Thu Jul 17 09:06:11 2025 +0000 @@ -1,17 +1,17 @@ -# This output was generated with AUGUSTUS (version 3.4.0). +# This output was generated with AUGUSTUS (version 3.5.0). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), -# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. +# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. # 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 # Sources of extrinsic information: M RM E W # Setting CDSpart local malus: 0.985 # Setting UTRpart local malus: 0.973 -# reading in the file /tmp/tmpb49zmbej/files/f/a/8/dataset_fa8684ad-0602-4c00-9999-b998db931a6e.dat ... +# reading in the file /tmp/tmpjsgft19_/files/2/8/2/dataset_2822734d-a594-477d-a8ef-82ffb21dcccf.dat ... # Have extrinsic information about 1 sequences (in the specified range). # Initializing the parameters using config directory /usr/local/config/ ... # fly version. Using default transition matrix. -# Looks like /tmp/tmpb49zmbej/files/4/c/8/dataset_4c80a809-791b-4afe-a497-698a7460ac31.dat is in fasta format. +# Looks like /tmp/tmpjsgft19_/files/6/d/9/dataset_6d9a0d6d-a406-4749-8cb1-1d06374faa38.dat is in fasta format. # We have hints for 1 sequence and for 1 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 2001, name = chr2R) ----- @@ -38,7 +38,6 @@ # start gene chr2R.g1 chr2R AUGUSTUS gene 7560 8931 0.84 - . chr2R.g1 chr2R AUGUSTUS transcript 7560 8931 0.84 - . chr2R.g1.t1 -chr2R AUGUSTUS start_codon 8929 8931 . - 0 transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1"; # Evidence for and against this transcript: # % of transcript supported by hints (any source): 60 # CDS exons: 3/3 @@ -53,4 +52,4 @@ # end gene chr2R.g1 ### # command line: -# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /tmp/tmpb49zmbej/files/4/c/8/dataset_4c80a809-791b-4afe-a497-698a7460ac31.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmpb49zmbej/files/f/a/8/dataset_fa8684ad-0602-4c00-9999-b998db931a6e.dat --extrinsicCfgFile=/tmp/tmpb49zmbej/files/3/3/5/dataset_335e9fec-9340-42e6-97ce-af35d5220fcc.dat --predictionStart=7000 --predictionEnd=9000 --species=fly +# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --start=off --stop=off --cds=off --singlestrand=false /tmp/tmpjsgft19_/files/6/d/9/dataset_6d9a0d6d-a406-4749-8cb1-1d06374faa38.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmpjsgft19_/files/2/8/2/dataset_2822734d-a594-477d-a8ef-82ffb21dcccf.dat --extrinsicCfgFile=/tmp/tmpjsgft19_/files/7/6/7/dataset_7673297f-b12d-48f2-b40c-2fcd8e18239d.dat --predictionStart=7000 --predictionEnd=9000 --species=fly
--- a/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf Sun Dec 15 09:09:49 2024 +0000 +++ b/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf Thu Jul 17 09:06:11 2025 +0000 @@ -1,13 +1,13 @@ -# This output was generated with AUGUSTUS (version 3.4.0). +# This output was generated with AUGUSTUS (version 3.5.0). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), -# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. +# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. # 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. # Initializing the parameters using config directory /usr/local/config/ ... # human version. Using default transition matrix. -# Looks like /tmp/tmpb49zmbej/files/c/d/6/dataset_cd6650af-fd36-4176-b9f1-e38bb118655f.dat is in fasta format. +# Looks like /tmp/tmpjsgft19_/files/b/3/0/dataset_b30bd3b8-32ff-49ce-be3d-bdb824bd72df.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) ----- @@ -98,4 +98,4 @@ # end gene HS08198.g2 ### # command line: -# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=on --start=on --stop=on --cds=on --singlestrand=false /tmp/tmpb49zmbej/files/c/d/6/dataset_cd6650af-fd36-4176-b9f1-e38bb118655f.dat --UTR=off --genemodel=complete --softmasking=0 --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/tmpjsgft19_/files/b/3/0/dataset_b30bd3b8-32ff-49ce-be3d-bdb824bd72df.dat --UTR=off --genemodel=complete --softmasking=0 --species=human
--- a/test-data/human_augustus_utr-on.gff Sun Dec 15 09:09:49 2024 +0000 +++ b/test-data/human_augustus_utr-on.gff Thu Jul 17 09:06:11 2025 +0000 @@ -1,14 +1,14 @@ ##gff-version 3 -# This output was generated with AUGUSTUS (version 3.4.0). +# This output was generated with AUGUSTUS (version 3.5.0). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), -# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. +# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. # 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. # Initializing the parameters using config directory /usr/local/config/ ... # human version. Using default transition matrix. -# Looks like /tmp/tmpb49zmbej/files/e/0/1/dataset_e0109fd4-ac59-4275-90d3-25691349bc0c.dat is in fasta format. +# Looks like /tmp/tmpjsgft19_/files/2/a/c/dataset_2acd78b6-6b4d-4592-91d1-ec3a4dc4a8f0.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) ----- @@ -19,7 +19,6 @@ 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 @@ -77,7 +76,6 @@ 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 @@ -103,4 +101,4 @@ # end gene HS08198.g2 ### # command line: -# augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpb49zmbej/files/e/0/1/dataset_e0109fd4-ac59-4275-90d3-25691349bc0c.dat --UTR=on --genemodel=complete --softmasking=0 --species=human +# augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --start=off --stop=off --cds=on --singlestrand=false /tmp/tmpjsgft19_/files/2/a/c/dataset_2acd78b6-6b4d-4592-91d1-ec3a4dc4a8f0.dat --UTR=on --genemodel=complete --softmasking=0 --species=human
--- a/test-data/human_augustus_utr-on.gtf Sun Dec 15 09:09:49 2024 +0000 +++ b/test-data/human_augustus_utr-on.gtf Thu Jul 17 09:06:11 2025 +0000 @@ -1,13 +1,14 @@ -# This output was generated with AUGUSTUS (version 3.4.0). +# Looks like /tmp/tmpjsgft19_/files/a/4/8/dataset_a48be2bb-95b9-461d-aa42-cc5ff0ce9360.dat is in gzip format. Deflating... +# This output was generated with AUGUSTUS (version 3.5.0). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), -# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. +# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. # 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. # Initializing the parameters using config directory /usr/local/config/ ... # human version. Using default transition matrix. -# Looks like /tmp/tmpb49zmbej/files/6/0/5/dataset_605b6f62-4302-4e11-b378-848be921c4e4.dat is in fasta format. +# Looks like /tmp/tmpjsgft19_/files/a/4/8/dataset_a48be2bb-95b9-461d-aa42-cc5ff0ce9360.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) ----- @@ -18,7 +19,6 @@ 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"; @@ -76,7 +76,6 @@ 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"; @@ -102,4 +101,4 @@ # end gene HS08198.g2 ### # command line: -# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpb49zmbej/files/6/0/5/dataset_605b6f62-4302-4e11-b378-848be921c4e4.dat --UTR=on --genemodel=complete --softmasking=0 --species=human +# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --start=off --stop=off --cds=on --singlestrand=false /tmp/tmpjsgft19_/files/a/4/8/dataset_a48be2bb-95b9-461d-aa42-cc5ff0ce9360.dat --UTR=on --genemodel=complete --softmasking=0 --species=human
--- a/test-data/human_augustus_utr-on_softmasking.gtf Sun Dec 15 09:09:49 2024 +0000 +++ b/test-data/human_augustus_utr-on_softmasking.gtf Thu Jul 17 09:06:11 2025 +0000 @@ -1,6 +1,6 @@ -# This output was generated with AUGUSTUS (version 3.4.0). +# This output was generated with AUGUSTUS (version 3.5.0). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), -# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. +# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. # 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 @@ -8,7 +8,7 @@ # Sources of extrinsic information: M RM # Initializing the parameters using config directory /usr/local/config/ ... # human version. Using default transition matrix. -# Looks like /tmp/tmpb49zmbej/files/1/1/4/dataset_11447207-979d-4b84-a63d-14dd1e776f0e.dat is in fasta format. +# Looks like /tmp/tmpjsgft19_/files/0/e/e/dataset_0ee7b75a-3ef6-4edb-811b-e06e2e5fae27.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) ----- @@ -21,4 +21,4 @@ # Predicted genes for sequence number 2 on both strands # (none) # command line: -# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpb49zmbej/files/1/1/4/dataset_11447207-979d-4b84-a63d-14dd1e776f0e.dat --UTR=on --genemodel=complete --softmasking=1 --species=human +# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --start=off --stop=off --cds=off --singlestrand=false /tmp/tmpjsgft19_/files/0/e/e/dataset_0ee7b75a-3ef6-4edb-811b-e06e2e5fae27.dat --UTR=on --genemodel=complete --softmasking=1 --species=human