diff getopt_specification.csv @ 6:5b07e567864b draft

planemo upload commit ee93fa730d90ffc1a895a849bdcb6050ed5ad2c9-dirty

--- a/getopt_specification.csv	Wed Apr 25 16:47:59 2018 -0400
+++ b/getopt_specification.csv	Wed Apr 25 17:20:11 2018 -0400
@@ -1,27 +1,9 @@
-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
\ No newline at end of file
+short flag,argument mask,data type,variable name
+o,1,character,report
+d,1,character,report.files_path
+A,1,character,genomeFastaFiles
+B,1,character,sjdbGTFfile
+C,1,character,sjdbOverhang
+F,1,character,first_reads
+R,1,character,second_reads
+S,1,character,sorted_bam
\ No newline at end of file