tools-iuc
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galaxyproject
kma: bump
CI is currently failing due to a core dump that happens if 2 slots are used
seems to be fixed in a newer version
new version seems to have quite some new options. will have no time to add them. anyone wants to jump in? would be cool to have them more structured in sections like in the CLI help output.
FOR CONTRIBUTOR:
- [x] - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
- [x] - License permits unrestricted use (educational + commercial)
- [ ] - This PR adds a new tool or tool collection
- [x] - This PR updates an existing tool or tool collection
- [ ] - This PR does something else (explain below)
Hi, I would try, but I can't estimate which parameters are useful and which to group. It would be very helpful if you could give me a short overview, otherwise I could also ask someone else to give me hints here and there.
Hi @mira-miracoli This is the CLI help:
# KMA-1.4.3 maps and/or aligns raw reads to a template database.
# Options: Desc: Default:
#
# Input:
# -i Single end input(s) stdin
# -ipe Paired end input(s)
# -int Interleaved input(s)
#
# Output:
# -o Output prefix
# -ef Output additional features False
# -vcf Output vcf file, 2 to apply FT False
# -sam Output sam, 4/2096 for mapped/aligned False
# -nc No consensus file False
# -na No aln file False
# -nf No frag file False
# -matrix Output assembly matrix False
# -a Output all template mappings False
# -and Use both mrs and p-value on consensus or
# -oa Use neither mrs or p-value on consensus False
# -tsv Tsv flag 0
# -tsvh Help on -tsv
#
# Consensus:
# -bc Minimum support to call bases 0
# -bcNano Altered indel calling for ONT data False
# -bcd Minimum depth to cal bases 1
# -bcg Maintain insignificant gaps False
# -ID Minimum consensus ID 1.0%
# -md Minimum depth 0.0
# -dense Skip insertion in consensus False
# -ref_fsa Use n's on indels False
#
# General:
# -t_db Template DB
# -p P-value 0.05
# -shm Use DB in shared memory 0
# -mmap Memory map *.comp.b False
# -tmp Set directory for temporary files
# -t Number of threads 1
# -status Extra status False
# -verbose Extra verbose False
# -c Citation
# -v Version
# -h Shows this help message
#
# Template mapping:
# -ConClave ConClave version 1
# -mem_mode Base ConClave on template mappings False
# -proxi Proximity scoring (negative for soft) False/1.0
# -ex_mode Searh kmers exhaustively False
# -deCon Remove contamination False
# -Sparse Only count kmers False
# -ss Sparse sorting (q,c,d) q
# -Mt1 Map everything to one template False/0
# -pm Pairing method (p,u,f) u
# -1t1 One query to one template False
# -hmm Use a HMM to assign template(s) False
# -ck Count k-mers over pseudo alignment False
# -localopen Penalty for openning a local chain 6
# -mct Max overlap between templates 0.1
# -lc Length corrected template chaining False
#
# Chaining:
# -k K-mersize DB defined
# -ts Trim front of seeds 0
# -ssa Seeds soround alignments False
# -ex_mode Searh kmers exhaustively False
# -fpm Pairing method (p,u,f) u
# -mq Minimum mapping quality 0
# -localopen Penalty for local opening 6
#
# Alignment:
# -ca Circular alignments False
# -mrs Minimum relative alignment score 0.5
# -mrc Minimum query coverage 0.0
# -ml Minimum alignment length 16
# -reward Score for match 1
# -penalty Penalty for mismatch 2
# -gapopen Penalty for gap opening 3
# -gapextend Penalty for gap extension 1
# -per Reward for pairing reads 7
# -Npenalty Penalty matching N 0
# -transition Penalty for transition 2
# -transversion Penalty for transversion 2
# -sasm Skip alignment False
#
# Trimming:
# -mp Minimum phred score 20
# -eq Minimum avg. quality score 0
# -5p Trim 5 prime 0
# -3p Trim 3 prime 0
# -ml Minimum length 16
# -xl Maximum length on se 2147483647
# -boot Bootstrap sub-sequence False
#
# Presets:
# -apm Sets both pm and fpm u
# -cge Set CGE penalties and rewards False
# -mint2 Set 2ng gen Mintyper preset False
# -mint3 Set 3rd gen Mintyper preset False
# -ont Set 3rd gen genefinding preset False
I really like the structuring which might be represented 1:1 as sections. Would be cool if you could do this. Then its also easier to see what is missing (maybe insert comments like <!-- TODO -paramXYZ -->). We can then discuss what should be included and what is optional...
Hi, I structured the params, I started only today because of holidays. Can you give me write access to this PR? And I am sorry but I cant continue working on this because of other tasks.
Hi @mira-miracoli I sent an invitation for collaboration to my fork.