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BackofenLab / GraphClust-2

A pipeline for structural clustering of RNA secondary structures
GNU General Public License v3.0
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Extend locarna wrapper parameters #24

Closed mmiladi closed 7 years ago

mmiladi commented 7 years ago

locARNAGraphClust.pl has a set of fixed parameters for calling LocARNA (OPTS_locarna_model, OPTS_locarna_maligs,..) that should be not set by default and be exposed to the user.

OPTS_locarna_maligs           -p 0.001 --max-diff-am 50 --tau 50 --alifold-consensus-dp --max-diff 100
OPTS_locarna_model            -p 0.001 --max-diff-am 50 --tau 50 --alifold-consensus-dp
OPTS_locarna_p_model          -p 0.001 --max-diff-am 50 --tau 50  --struct-weight 160 --plfold-span 150 --plfold-winsize 200 --temperature 180 --mea-beta 400 --consistency-transformation