diff --git a/README.md b/README.md index d8d9cfb..97e8bd1 100644 --- a/README.md +++ b/README.md @@ -30,16 +30,16 @@ export PATH=$PATH:/home/Programms/hmmer-3.1b2-linux-intel-x86_64/binaries ``` ./TriPepSVM.sh [OPTION] ... -i INPUT.[fasta|fa] --i,\t--input [INPUT.fasta|fa]: AA sequence in fasta format, NO DEFAULT --o,\t--output : path to output folder, DEFAULT: current directory --id,\t--taxon-id [9606|590|...] : Uniprot taxon id, DEFAULT: 9606 (human) --c,\t--cost : change COST parameter, DEFAULT: 1 --k,\t--oligo-length : change k parameter, DEFAULT: 3 --pos,\t--pos-class : change positive class weight, DEFAULT: inverse proportional to class size --neg,\t--neg-class : change negative class weight, DEFAULT: inverse proportional to class size --thr,\t--threshold : change prediction threshold, DEFAULT: 0 --r,\t--recursive [TRUE|FALSE]: apply recursive mode, DEFAULT: FALSE --h,\t--help : help text +-i, --input [INPUT.fasta|fa]: AA sequence in fasta format, NO DEFAULT +-o, --output : path to output folder, DEFAULT: current directory +-id, --taxon-id [9606|590|...] : Uniprot taxon id, DEFAULT: 9606 (human) +-c, --cost : change COST parameter, DEFAULT: 1 +-k, --oligo-length : change k parameter, DEFAULT: 3 +-pos, --pos-class : change positive class weight, DEFAULT: inverse proportional to class size +-neg, --neg-class : change negative class weight, DEFAULT: inverse proportional to class size +-thr, --threshold : change prediction threshold, DEFAULT: 0 +-r, --recursive [TRUE|FALSE]: apply recursive mode, DEFAULT: FALSE +-h, --help : help text ``` Example 1: Salmonella