short flag,argument mask,data type,variable name
o,1,character,report
d,1,character,report.files_path
A,1,character,first_reads
B,1,character,second_reads
x,1,character,adapter_first_reads
y,1,character,adapter_second_reads
m,1,character,trimming_mode
r,1,character,maximum_allowed_error_rate
D,1,character,maximum_allowed_indel_error_rate
q,1,character,quality_trimming_3_end
Q,1,character,mean_quality
l,1,character,minimum_read_length
j,1,character,advanced_options.junction_adapter
M,1,character,advanced_options.tab_adapter
b,1,character,advanced_options.barcode
c,1,character,advanced_options.cut
n,1,character,advanced_options.filter_degenerative_reads
u,1,character,advanced_options.filter_undetermined_mate_pair_reads
f,1,character,advanced_options.format
z,1,character,advanced_options.compress
E,1,character,advanced_options.qiime
F,1,character,advanced_options.quiet
i,1,character,advanced_options.intelligent
1,1,character,trimmed_r1
2,1,character,trimmed_r2
3,1,character,trimmed_s