view getopt_specification.csv @ 2:d9601e1eb360 draft

v1.1.0

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