funannotate annotate: missing options in help?

[xvazquezc]

Are you using the latest release? Installed from master

Describe the bug Some of the options indicated in some threads are not displayed with the help. e.g. I was looking at #650 (re: SignalP 6 support), but the mentioned --signalp is no displayed by any of the commands help. For what I could find, it seems that the displayed help is drawn from funannotate/funannotate.py but it doesn't match all the options encoded/supported by funannotate/annotate.py

EDIT: the options I found missing from funannotate annotate --help are --signalp, --p2g, and --header_length.

What command did you issue? funannotate annotate and funannotate annotate --help, same result.

Logfiles

$ funannotate annotate --help

Usage:       funannotate annotate <arguments>
version:     1.8.10

Description: Script functionally annotates the results from funannotate predict.  It pulls
             annotation from PFAM, InterPro, EggNog, UniProtKB, MEROPS, CAZyme, and GO ontology.

Required:
  -i, --input          Folder from funannotate predict
    or
  --genbank            Genome in GenBank format
  -o, --out            Output folder for results
    or
  --gff                Genome GFF3 annotation file
  --fasta              Genome in multi-fasta format
  -s, --species        Species name, use quotes for binomial, e.g. "Aspergillus fumigatus"
  -o, --out            Output folder for results

Optional:
  --sbt                NCBI submission template file. (Recommended)
  -a, --annotations    Custom annotations (3 column tsv file)
  -m, --mito-pass-thru Mitochondrial genome/contigs. append with :mcode
  --eggnog             Eggnog-mapper annotations file (if NOT installed)
  --antismash          antiSMASH secondary metabolism results (GBK file from output)
  --iprscan            InterProScan5 XML file
  --phobius            Phobius pre-computed results (if phobius NOT installed)
  --isolate            Isolate name
  --strain             Strain name
  --rename             Rename GFF gene models with locus_tag from NCBI.
  --fix                Gene/Product names fixed (TSV: GeneID	Name	Product)
  --remove             Gene/Product names to remove (TSV: Gene	Product)
  --busco_db           BUSCO models. Default: dikarya
  -t, --tbl2asn        Additional parameters for tbl2asn. Default: "-l paired-ends"
  -d, --database       Path to funannotate database. Default: $FUNANNOTATE_DB
  --force              Force over-write of output folder
  --cpus               Number of CPUs to use. Default: 2
  --tmpdir             Volume/location to write temporary files. Default: /tmp
  --no-progress        Do not print progress to stdout for long sub jobs

OS/Install Information

-------------------------------------------------------
Checking dependencies for 1.8.10
-------------------------------------------------------
You are running Python v 3.8.12. Now checking python packages...
biopython: 1.77
goatools: 1.2.3
matplotlib: 3.4.3
natsort: 8.1.0
numpy: 1.22.3
pandas: 1.4.2
psutil: 5.9.0
requests: 2.27.1
scikit-learn: 1.0.2
scipy: 1.8.0
seaborn: 0.11.2
All 11 python packages installed


You are running Perl v b'5.026002'. Now checking perl modules...
Bio::Perl: 1.007002
Carp: 1.38
Clone: 0.42
DBD::SQLite: 1.64
DBD::mysql: 4.046
DBI: 1.642
DB_File: 1.855
Data::Dumper: 2.173
File::Basename: 2.85
File::Which: 1.23
Getopt::Long: 2.5
Hash::Merge: 0.300
JSON: 4.02
LWP::UserAgent: 6.15
Logger::Simple: 2.0
POSIX: 1.76
Parallel::ForkManager: 2.02
Pod::Usage: 1.69
Scalar::Util::Numeric: 0.40
Storable: 3.15
Text::Soundex: 3.05
Thread::Queue: 3.12
Tie::File: 1.02
URI::Escape: 3.31
YAML: 1.29
local::lib: 2.000024
threads: 2.15
threads::shared: 1.56
All 28 Perl modules installed


Checking Environmental Variables...
$PASAHOME=/home/z3382651/miniconda3/envs/funannotate-master/opt/pasa-2.4.1
$TRINITY_HOME=/home/z3382651/miniconda3/envs/funannotate-master/opt/trinity-2.8.5
$EVM_HOME=/home/z3382651/miniconda3/envs/funannotate-master/opt/evidencemodeler-1.1.1
$AUGUSTUS_CONFIG_PATH=/home/z3382651/miniconda3/envs/funannotate-master/config/
	ERROR: FUNANNOTATE_DB not set. export FUNANNOTATE_DB=/path/to/dir
	ERROR: GENEMARK_PATH not set. export GENEMARK_PATH=/path/to/dir
-------------------------------------------------------
Checking external dependencies...
PASA: 2.4.1
CodingQuarry: 2.0
Trinity: 2.8.5
augustus: 3.3.3
bamtools: bamtools 2.5.1
bedtools: bedtools v2.30.0
blat: BLAT v36
diamond: 2.0.14
ete3: 3.1.2
exonerate: exonerate 2.4.0
fasta: no way to determine
glimmerhmm: 3.0.4
gmap: 2017-11-15
hisat2: 2.2.1
hmmscan: HMMER 3.3.2 (Nov 2020)
hmmsearch: HMMER 3.3.2 (Nov 2020)
java: 11.0.13
kallisto: 0.46.1
mafft: v7.505 (2022/Apr/10)
makeblastdb: makeblastdb 2.2.31+
minimap2: 2.24-r1122
pigz: pigz 2.6
proteinortho: 6.0.34
pslCDnaFilter: no way to determine
salmon: salmon 0.14.1
samtools: samtools 1.12
signalp: 5.0b
snap: 2006-07-28
stringtie: 2.2.1
tRNAscan-SE: 2.0.9 (July 2021)
tantan: tantan 31
tbl2asn: no way to determine, likely 25.X
tblastn: tblastn 2.2.31+
trimal: trimAl v1.4.rev15 build[2013-12-17]
trimmomatic: 0.39
	ERROR: emapper.py not installed
	ERROR: gmes_petap.pl not installed