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annotate test-data/human_augustus_utr-on_softmasking.gtf @ 8:aada0deea587 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 69d542836dbce9261906bb0d1e7ef39f9712f4a3
author iuc
date Sun, 15 Dec 2024 09:09:49 +0000
parents 7be22100e5e1
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7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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1 # This output was generated with AUGUSTUS (version 3.4.0).
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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2 # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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3 # O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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4 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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5 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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6 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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7 # No extrinsic information on sequences given.
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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8 # Sources of extrinsic information: M RM
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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9 # Initializing the parameters using config directory /usr/local/config/ ...
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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10 # human version. Using default transition matrix.
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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11 # Looks like /tmp/tmpb49zmbej/files/1/1/4/dataset_11447207-979d-4b84-a63d-14dd1e776f0e.dat is in fasta format.
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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12 # We have hints for 0 sequences and for 0 of the sequences in the input set.
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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13 #
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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14 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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15 #
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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16 # Predicted genes for sequence number 1 on both strands
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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17 # (none)
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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18 #
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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19 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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20 #
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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21 # Predicted genes for sequence number 2 on both strands
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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22 # (none)
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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23 # command line:
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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24 # 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