Mercurial > repos > bgruening > augustus
diff test-data/human_augustus_protein_codingseq_introns_cds_main.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 |
line wrap: on
line diff
--- a/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf Sun Dec 15 09:09:57 2024 +0000 +++ b/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf Thu Jul 17 09:06:01 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