diff rmarkdown_feature_counts_render.R @ 7:7857bfd9d604 draft

update

--- a/rmarkdown_feature_counts_render.R	Thu Dec 28 16:56:01 2017 -0500
+++ b/rmarkdown_feature_counts_render.R	Thu Dec 28 22:07:13 2017 -0500
@@ -2,6 +2,7 @@
 library(rmarkdown)
 library(htmltools)
 library(dplyr)
+library(Rsubread)
 
 ##============ Sink warnings and errors to a file ==============
 ## use the sink() function to wrap all code within it.
@@ -32,6 +33,40 @@
   args_list=list()
   ##------- 1. input data ---------------------
   args_list$ECHO = c('echo', 'e', '1', 'character')
+  args_list$b = c('input_bam', 'b', '1', 'character')
+  args_list$c = c('annot_ext', 'c', '1', 'character')
+  args_list$f = c('isGTFAnnotationFile', 'f', '1', 'character')
+  args_list$g = c('gtf_feature_type', 'g', '1', 'character')
+  args_list$h = c('gtf_attr_type', 'h', '1', 'character')
+  args_list$i = c('chr_aliases', 'i', '1', 'character')
+  args_list$j = c('use_meta_features', 'j', '1', 'character')
+  args_list$k = c('allow_multi_overlap', 'k', '1', 'character')
+  args_list$l = c('min_overlap', 'l', '1', 'character')
+  args_list$m = c('largest_overlap', 'm', '1', 'character')
+  args_list$n = c('read_extension_5', 'n', '1', 'character')
+  args_list$o = c('read_extension_3', 'o', '1', 'character')
+  args_list$p = c('read_2_pos', 'p', '1', 'character')
+  args_list$q = c('count_multi_mapping_reads', 'q', '1', 'character')
+  args_list$u = c('fraction', 'u', '1', 'character')
+  args_list$v= c('min_mqs', 'v', '1', 'character')
+  args_list$w= c('split_only', 'w', '1', 'character')
+  args_list$x= c('non_split_only', 'x', '1', 'character')
+  args_list$y= c('primary_only', 'y', '1', 'character')
+  args_list$z= c('ignore_dup', 'z', '1', 'character')
+  args_list$A= c('strand_specific', 'A', '1', 'character')
+  args_list$B= c('junc_counts', 'B', '1', 'character')
+  args_list$C= c('genome', 'C', '1', 'character')
+  args_list$D= c('is_paired_end', 'D', '1', 'character')
+  args_list$E= c('require_both_ends_mapped', 'E', '1', 'character')
+  args_list$F= c('check_frag_length', 'F', '1', 'character')
+  args_list$G= c('min_frag_length', 'G', '1', 'character')
+  args_list$H= c('max_frag_length', 'H', '1', 'character')
+  args_list$I= c('count_chimeric_fragments', 'I', '1', 'character')
+  args_list$J= c('auto_sort', 'J', '1', 'character')
+  args_list$K= c('n_threads', 'K', '1', 'character')
+  args_list$L= c('max_mop', 'L', '1', 'character')
+  args_list$M= c('report_reads', 'M', '1', 'character')
+  
   ##--------2. output report and outputs --------------
   args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
   args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')