diff getopt_specification.csv @ 2:d9601e1eb360 draft

v1.1.0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getopt_specification.csv	Sun Mar 18 11:07:16 2018 -0400
@@ -0,0 +1,28 @@
+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,
\ No newline at end of file