annotate test-data/human_augustus_utr-on_softmasking.gtf @ 9:2fdc599f2814 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782

# This output was generated with AUGUSTUS (version 3.5.0).
# AUGUSTUS is a gene prediction tool written by M. Stanke ([e-mail]),
# 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.
# Sources of extrinsic information: M RM 
# Initializing the parameters using config directory /usr/local/config/ ...
# human version. Using default transition matrix.
# 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) -----
#
# Predicted genes for sequence number 1 on both strands
# (none)
#
# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
#
# Predicted genes for sequence number 2 on both strands
# (none)
# command line:
# 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