Mercurial > repos > bgruening > augustus
diff test-data/human_augustus_utr-on.gtf @ 11:534814b64234 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 09:06:01 +0000 |
| parents | 09855551d713 |
| children |
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--- a/test-data/human_augustus_utr-on.gtf Sun Dec 15 09:09:57 2024 +0000 +++ b/test-data/human_augustus_utr-on.gtf Thu Jul 17 09:06:01 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